What is GATK?
Simply what it says on the can: a Toolkit for Genome Analysis


More specifically, it's a toolkit for variant discovery.

The GATK is the industry standard for identifying SNPs and indels in germline DNA and RNAseq data, and its scope is currently being extended to include somatic variant calling tools. In addition to the variant callers themselves, the GATK also includes many utilities to perform related tasks such as processing and quality control of high-throughput sequencing data.

The GATK tools are primarily designed to process exomes and whole genomes generated with Illumina sequencing technology, but they can be adapted to handle a variety of other technologies and experimental designs. And although it was originally developed for human genetics, the GATK has since evolved to handle genome data from any organism, with any level of ploidy.

Organisms

The GATK can handle a variety of organism genomes in addition to humans.

GATK engine and walkers

The toolkit provides a wide set of tools that can be chained into workflows, taking advantage of the common architecture and powerful engine.

 

So what's in the can?

At the heart of the GATK is an industrial-strength infrastructure and engine that handle data access, conversion and traversal, as well as high-performance computing features. On top of that lives a rich ecosystem of specialized tools, called walkers, that you can use out of the box, individually or chained into scripted workflows, to perform anything from simple data diagnostics to complex reads-to-results analyses. See the Tool Docs for a complete list of tools and their capabilities.

Built for high performance

Many GATK tools can be parallelized by multithreading, and the toolkit also comes with a companion program called Queue that enables easy parallelization on a high-performance computing cluster or server farm. See this article for more details on parallelism with the GATK.

The world-famous GATK Best Practices

When you're isolating DNA in the lab, you don't treat the work like isolated, disconnected tasks. Every task is a step in a well-documented protocol, carefully developed to optimize yield, purity and to ensure reproducibility as well as consistency across all samples and experiments. We believe working with the sequencing data should be treated in the same thorough manner.

That's why GATK comes with complete reads-to-results variant discovery workflow recommendations, battle-tested and optimized to produce the most accurate results with the most computational efficiency.

These Best Practices are used in production at the Broad Institute on every genome or exome that rolls out of the sequencing facility. See the documentation for more detail.

Best Practices workflow

Best Practices for variant discovery in germline DNA leveraging the groundbreaking methods for combined power and scalability introduced in GATK 3.



Using GATK

 

Using GATK
Get started today


Platform and requirements

The GATK is designed to run on Linux and other POSIX-compatible platforms. Yes, that includes MacOS X! If you are on any of the above, see the Downloads section for downloading and installation instructions. If you're stuck with Windows, you're not completely out of luck – it's possible to use the GATK with Cygwin, although we can't provide any specific support for that. If you're on something else... no, there are no plans to port the GATK to Android or iOS in the near future.

You will need to have Java installed to run the GATK, and some tools additionally require R to generate PDF plots. Version requirements and installation instructions for both can be found in the Documentation Guide.

Unix-based operating systems

The GATK is designed to run on Linux and other POSIX-compatible platforms, including MacOS X.

Interface

Now here's the catch: the GATK does not have a graphical user interface. All tools are called via the command-line interface.

If that is not something you are used to, or you have no idea what that even means, don't worry. It's easier to learn than you might think, and there are many good online tutorials that can get help you get comfortable with the command-line environment. Before you know it you'll be writing scripts to chain tools together into workflows... You don't need to have any programming experience to use the GATK, but you might pick some up along the way!

Output of the example command

The GATK outputs structured command information, status messages and result summaries to the console.

Command structure and tool arguments

All the GATK tools are called using the same basic command structure. Here's a simple example that counts the number of sequence reads in a BAM file:

java -jar GenomeAnalysisTK.jar \
-T CountReads \
-R example_reference.fasta \
-I example_reads.bam \
    -o

The -jar argument invokes the GATK engine itself, and the -T argument tells it which tool you want to run. Arguments like -R for the genome reference and -I for the input file are also given to the GATK engine and can be used with all the tools (see complete list of available arguments for the GATK engine. Most tools also take additional arguments that are specific to their function. These are listed for each tool on that tool's documentation page, all easily accessible through the Tool Documentation index.

The GATK runs on Java


The GATK runs on Java, straight from the command-line.


What is GATK? Getting Help

 

Getting Help
Don't panic! Help is at hand.


The GATK has a reputation for being wicked complicated, and it's not entirely undeserved. With great power comes great responsibility complexity... But don't panic! Help is at hand.

Our crack team of tech support monkeys has put together a complete documentation and support system to help you get the answers you need, fast and with the least amount of pain. It's composed of reference guides, tutorials, videos and a forum that are all cross-connected, so that relevant material from various sources is automatically aggregated for you, whether you're browsing an index or searching by keyword.

All that time you'll save on looking for information and troubleshooting? Feel free to use it to get even more work done... or finally get out of the lab and have a life!


The Hitchhiker's Guide to the GATK


If you've ever wondered "Is there a tool that can do X?" or "Does this tool have an argument to do Y?", the Tool Documentation should be your first stop. Every tool in the GATK has its own webpage detailing what it does and how it does it, as well as all the available options, default parameter values and argument names.

In addition to this tool-oriented technical documentation, the Guide also features articles detailing Methods and Algorithms and our widely adopted Best Practices recommendations for study design and analysis.

FAQs, tutorials and videos


The Guide is further enriched by a regularly updated collection of Frequently Asked Questions and solutions to Common Problems, as well as Tutorials that explain step by step how to run the tools and apply our workflow recommendations.

Be sure to also check out the Presentations from our recurring workshop series. In addition to the presentation slide decks, we provide recordings of the workshops that we hold at the Broad; you can view them on the Broad website or on the Broad education channels on YouTube and iTunesU.

Community forum


Finally, if you've exhausted all these avenues and still haven't found the answer to your question, ask the forum! It's powered by rainbows and staffed by unicorns who love to answer USER ERROR questions.

Well, maybe not unicorns, but a team of computational biologists and software engineers who work hard to address your problems quickly and accurately. If something's not clearly documented, we'll answer you question and improve the docs accordingly. If you think you found a bug, we'll track it down and fix it. Just Ask the Team.


Using GATK Licensing & Source Code

 

Licensing & Source Code


Free for academics, fee for commercial use

The GATK and its sister program, MuTect, are increasingly used not just in academic research, but also in clinical and commercial production environments. In order to sustain a development team that can meet the high standards required for the quality of the software itself as well as the support that we provide, we release GATK and MuTect under a mixed licensing model. This means that researchers at academic and non-profit organizations can access the tools and source code for free, while for-profit organizations are required to purchase a license. The revenue generated by this model is then used to fund and build out our support team and infrastructure to accommodate the demand for support in the community, as well as invest more resources to improve development speed, functionality and stability overall. The text of the academic license can be viewed here.

Direct licensing and support through Broad

As of April 16, 2015, we are providing licensing and support directly to commercial/for-profit organizations that will be running the GATK or MuTect internally or as part of their own hardware offering. This new licensing arrangement will allow licensed customers better access to the GATK and MuTect development and support teams, full support for the latest releases of our tools, and the most up-to-date Best Practice recommendations that are based on our team's extensive analysis and R&D work. Users who currently hold a license purchased through our former commercial partner, Appistry, will continue to be supported by Appistry until their license expires, at which time they will have the opportunity to renew their license through the Broad Institute. All users are welcome to enjoy the support we offer for free through the forum.



For more information about the licensing and the recent transition from Appistry to direct-through-Broad licensing, please read our announcement on the GATK blog or contact softwarelicensing@broadinstitute.org directly with any questions about licensing, pricing or the availability of premium support.


Getting Help User Testimonials

 

User Testimonials
How GATK makes a difference in the real world



Share your story

How has the GATK made a difference in your work? If you would like to share your story, leave us a note in the forum.


Licensing & Source Code In the Literature

 

In the Literature
Use of GATK in peer-reviewed studies.


This is a list of 201 publications that illustrate successful applications of GATK to research questions. It is not meant to be exhaustive, and comprises only papers published since 2010 in the following journals: Nature, Science, Nature Genetics, Nature Biotechnology, New England Journal of Medicine, Cell, and Genome Research.


Genomic analysis identifies new drivers and progression pathways in skin basal cell carcinoma
Bonilla, Ximena et al., 2016 NATURE GENETICS [Article] [Pubmed]

Inactivating Variants in ANGPTL4 and Risk of Coronary Artery Disease
Dewey, Frederick F. et al., 2016 NEW ENGLAND JOURNAL OF MEDICINE [Article] [Pubmed]

Frequent somatic CDH1 loss-of-function mutations in plasmacytoid variant bladder cancer
Al-Ahmadie, Hikmat A. et al., 2016 NATURE GENETICS [Article] [Pubmed]

Ancient gene flow from early modern humans into Eastern Neanderthals
Kuhlwilm, Martin et al., 2016 NATURE [Article] [Pubmed]

Haplotyping germline and cancer genomes with high-throughput linked-read sequencing
Zheng, Grace X. Y. et al., 2016 NATURE BIOTECHNOLOGY [Article] [Pubmed]

Divergent clonal selection dominates medulloblastoma at recurrence
Morrissy, A. Sorana et al., 2016 NATURE [Article] [Pubmed]

Structural genomic changes underlie alternative reproductive strategies in the ruff (Philomachus pugnax)
Lamichhaney, Sangeet et al., 2016 NATURE GENETICS [Article] [Pubmed]

The genomic landscape of juvenile myelomonocytic leukemia
Stieglitz, Elliot et al., 2015 NATURE GENETICS [Article] [Pubmed]

Alternative transcription initiation leads to expression of a novel ALK isoform in cancer
Wiesner, Thomas et al., 2015 NATURE [Article] [Pubmed]

The genome of the vervet (Chlorocebus aethiops sabaeus)
Warren, Wesley C. et al., 2015 GENOME RESEARCH [Article] [Pubmed]

BET inhibitor resistance emerges from leukaemia stem cells
Fong, Chun Yew et al., 2015 NATURE [Article] [Pubmed]

Linked selection and recombination rate variation drive the evolution of the genomic landscape of differentiation across the speciation continuum of Ficedula flycatchers
Burri, Reto et al., 2015 GENOME RESEARCH [Article] [Pubmed]

Tandem repeat variation in human and great ape populations and its impact on gene expression divergence
Sonay, Tugce Bilgin et al., 2015 GENOME RESEARCH [Article] [Pubmed]

Extensive de novo mutation rate variation between individuals and across the genome of Chlamydomonas reinhardtii
Ness, Rob W. et al., 2015 GENOME RESEARCH [Article] [Pubmed]

Genomic analysis of mycosis fungoides and Sezary syndrome identifies recurrent alterations in TNFR2
Ungewickell, Alexander et al., 2015 NATURE GENETICS [Article] [Pubmed]

The use of exome capture RNA-seq for highly degraded RNA with application to clinical cancer sequencing
Cieslik, Marcin et al., 2015 GENOME RESEARCH [Article] [Pubmed]

Genomics and drug profiling of fatal TCF3-HLF-positive acute lymphoblastic leukemia identifies recurrent mutation patterns and therapeutic options
Fischer, Ute et al., 2015 NATURE GENETICS [Article] [Pubmed]

Chimeric EWSR1-FLI1 regulates the Ewing sarcoma susceptibility gene EGR2 via a GGAA microsatellite
Gruenewald, Thomas G. P. et al., 2015 NATURE GENETICS [Article] [Pubmed]

Lanosterol reverses protein aggregation in cataracts
Zhao, Ling et al., 2015 NATURE [Article] [Pubmed]

Genetic evidence for two founding populations of the Americas
Skoglund, Pontus et al., 2015 NATURE [Article] [Pubmed]

Exome sequencing identifies somatic mutations of DDX3X in natural killer/T-cell lymphoma
Jiang, Lu et al., 2015 NATURE GENETICS [Article] [Pubmed]

Parent-progeny sequencing indicates higher mutation rates in heterozygotes
Yang, Sihai et al., 2015 NATURE [Article] [Pubmed]

Sparse whole-genome sequencing identifies two loci for major depressive disorder
Cai, Na et al., 2015 NATURE [Article] [Pubmed]

Germline mutation rates and the long-term phenotypic effects of mutation accumulation in wild-type laboratory mice and mutator mice
Uchimura, Arikuni et al., 2015 GENOME RESEARCH [Article] [Pubmed]

Relapsed neuroblastomas show frequent RAS-MAPK pathway mutations
Eleveld, Thomas F. et al., 2015 NATURE GENETICS [Article] [Pubmed]

Rare A2ML1 variants confer susceptibility to otitis media
Santos-Cortez, Regie Lyn P. et al., 2015 NATURE GENETICS [Article] [Pubmed]

Loss-of-function variants in ATM confer risk of gastric cancer
Helgason, Hannes et al., 2015 NATURE GENETICS [Article] [Pubmed]

Massively parallel quantification of the regulatory effects of noncoding genetic variation in a human cohort
Vockley, Christopher M. et al., 2015 GENOME RESEARCH [Article] [Pubmed]

Whole-genome characterization of chemoresistant ovarian cancer
Patch, Ann-Marie et al., 2015 NATURE [Article] [Pubmed]

Comprehensive models of human primary and metastatic colorectal tumors in immunodeficient and immunocompetent mice by chemokine targeting
Chen, Huanhuan Joyce et al., 2015 NATURE BIOTECHNOLOGY [Article] [Pubmed]

De novo assembly of a haplotype-resolved human genome
Cao, Hongzhi et al., 2015 NATURE BIOTECHNOLOGY [Article] [Pubmed]

Prospective Derivation of a Living Organoid Biobank of Colorectal Cancer Patients
van de Wetering, Marc et al., 2015 CELL [Article] [Pubmed]

Sequential cancer mutations in cultured human intestinal stem cells
Drost, Jarno et al., 2015 NATURE [Article] [Pubmed]

Biallelic mutations in SNX14 cause a syndromic form of cerebellar atrophy and lysosome-autophagosome dysfunction
Akizu, Naiara et al., 2015 NATURE GENETICS [Article] [Pubmed]

Loss of delta-catenin function in severe autism
Turner, Tychele N. et al., 2015 NATURE [Article] [Pubmed]

The Paf1 complex represses small-RNA-mediated epigenetic gene silencing
Kowalik, Katarzyna Maria et al., 2015 NATURE [Article] [Pubmed]

Large-scale whole-genome sequencing of the Icelandic population
Gudbjartsson, Daniel F. et al., 2015 NATURE GENETICS [Article] [Pubmed]

Germline mutations in ETV6 are associated with thrombocytopenia, red cell macrocytosis and predisposition to lymphoblastic leukemia
Noetzli, Leila et al., 2015 NATURE GENETICS [Article] [Pubmed]

Quality score compression improves genotyping accuracy
Yu, Y. William et al., 2015 NATURE BIOTECHNOLOGY [Article] [Pubmed]

Polyploidy can drive rapid adaptation in yeast
Selmecki, Anna M. et al., 2015 NATURE [Article] [Pubmed]

Germline gain-of-function mutations in AFF4 cause a developmental syndrome functionally linking the super elongation complex and cohesin
Izumi, Kosuke et al., 2015 NATURE GENETICS [Article] [Pubmed]

Stromal gene expression defines poor-prognosis subtypes in colorectal cancer
Calon, Alexandre et al., 2015 NATURE GENETICS [Article] [Pubmed]

The genomic and phenotypic diversity of Schizosaccharomyces pombe
Jeffares, Daniel C. et al., 2015 NATURE GENETICS [Article] [Pubmed]

Whole-genome and multisector exome sequencing of primary and post-treatment glioblastoma reveals patterns of tumor evolution
Kim, Hoon et al., 2015 GENOME RESEARCH [Article] [Pubmed]

Resequencing 302 wild and cultivated accessions identifies genes related to domestication and improvement in soybean
Zhou, Zhengkui et al., 2015 NATURE BIOTECHNOLOGY [Article] [Pubmed]

Combined hereditary and somatic mutations of replication error repair genes result in rapid onset of ultra-hypermutated cancers
Shlien, Adam et al., 2015 NATURE GENETICS [Article] [Pubmed]

Adaptation and possible ancient interspecies introgression in pigs identified by whole-genome sequencing
Ai, Huashui et al., 2015 NATURE GENETICS [Article] [Pubmed]

Large multiallelic copy number variations in humans
Handsaker, Robert E. et al., 2015 NATURE GENETICS [Article] [Pubmed]

Genetic and phenotypic intra-species variation in Candida albicans
Hirakawa, Matthew P. et al., 2015 GENOME RESEARCH [Article] [Pubmed]

Exome sequencing identifies rare LDLR and APOA5 alleles conferring risk for myocardial infarction
Do, Ron et al., 2015 NATURE [Article] [Pubmed]

Convergent loss of PTEN leads to clinical resistance to a PI(3)K alpha inhibitor
Juric, Dejan et al., 2015 NATURE [Article] [Pubmed]

Spectrum of diverse genomic alterations define non-clear cell renal carcinoma
Durinck, Steffen et al., 2015 NATURE GENETICS [Article] [Pubmed]

Convergent evolution and adaptation of Pseudomonas aeruginosa within patients with cystic fibrosis
Marvig, Rasmus Lykke et al., 2015 NATURE GENETICS [Article] [Pubmed]

A recurrent de novo mutation in KCNC1 causes progressive myoclonus epilepsy
Muona, Mikko et al., 2015 NATURE GENETICS [Article] [Pubmed]

The mutational landscapes of genetic and chemical models of Kras-driven lung cancer
Westcott, Peter M. K. et al., 2015 NATURE [Article] [Pubmed]

A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping
Rao, Suhas S. P. et al., 2014 CELL [Article] [Pubmed]

Predicting immunogenic tumour mutations by combining mass spectrometry and exome sequencing
Yadav, Mahesh et al., 2014 NATURE [Article] [Pubmed]

The contribution of de novo coding mutations to autism spectrum disorder
Iossifov, Ivan et al., 2014 NATURE [Article] [Pubmed]

Synaptic, transcriptional and chromatin genes disrupted in autism
De Rubeis, Silvia et al., 2014 NATURE [Article] [Pubmed]

Rapid modelling of cooperating genetic events in cancer through somatic genome editing
Sanchez-Rivera, Francisco J. et al., 2014 NATURE [Article] [Pubmed]

Estimating genotype error rates from high-coverage next-generation sequence data
Wall, Jeffrey D. et al., 2014 GENOME RESEARCH [Article] [Pubmed]

Large-scale identification of chemically induced mutations in Drosophila melanogaster
Haelterman, Nele A. et al., 2014 GENOME RESEARCH [Article] [Pubmed]

Ancient human genomes suggest three ancestral populations for present-day Europeans
Lazaridis, Iosif et al., 2014 NATURE [Article] [Pubmed]

Multi-platform assessment of transcriptome profiling using RNA-seq in the ABRF next-generation sequencing study
Li, Sheng et al., 2014 NATURE BIOTECHNOLOGY [Article] [Pubmed]

Clonal evolution in breast cancer revealed by single nucleus genome sequencing
Wang, Yong et al., 2014 NATURE [Article] [Pubmed]

A common Greenlandic TBC1D4 variant confers muscle insulin resistance and type 2 diabetes
Moltke, Ida et al., 2014 NATURE [Article] [Pubmed]

Integrating mapping-, assembly- and haplotype-based approaches for calling variants in clinical sequencing applications
Rimmer, Andy et al., 2014 NATURE GENETICS [Article] [Pubmed]

Whole-genome sequence variation, population structure and demographic history of the Dutch population
Francioli, Laurent C. et al., 2014 NATURE GENETICS [Article] [Pubmed]

Population genomics of parallel hybrid zones in the mimetic butterflies, H. melpomene and H. erato
Nadeau, Nicola J. et al., 2014 GENOME RESEARCH [Article] [Pubmed]

CLP1 Founder Mutation Links tRNA Splicing and Maturation to Cerebellar Development and Neurodegeneration
Schaffer, Ashleigh E. et al., 2014 CELL [Article] [Pubmed]

Somatic mutations found in the healthy blood compartment of a 115-yr-old woman demonstrate oligoclonal hematopoiesis
Holstege, Henne et al., 2014 GENOME RESEARCH [Article] [Pubmed]

Domains of genome-wide gene expression dysregulation in Down's syndrome
Letourneau, Audrey et al., 2014 NATURE [Article] [Pubmed]

Identification of genomic alterations in oesophageal squamous cell cancer
Song, Yongmei et al., 2014 NATURE [Article] [Pubmed]

Mutations in TJP2 cause progressive cholestatic liver disease
Sambrotta, Melissa et al., 2014 NATURE GENETICS [Article] [Pubmed]

doublesex is a mimicry supergene
Kunte, K. et al., 2014 NATURE [Article] [Pubmed]

A recurrent inactivating mutation in RHOA GTPase in angioimmunoblastic T cell lymphoma
Yoo, Hae Yong et al., 2014 NATURE GENETICS [Article] [Pubmed]

A cascade of DNA-binding proteins for sexual commitment and development in Plasmodium
Sinha, Abhinav et al., 2014 NATURE [Article] [Pubmed]

Integrating human sequence data sets provides a resource of benchmark SNP and indel genotype calls
Zook, Justin M. et al., 2014 NATURE BIOTECHNOLOGY [Article] [Pubmed]

Evolution and transmission of drug-resistant tuberculosis in a Russian population
Casali, Nicola et al., 2014 NATURE GENETICS [Article] [Pubmed]

Derived immune and ancestral pigmentation alleles in a 7,000-year-old Mesolithic European
Olalde, Inigo et al., 2014 NATURE [Article] [Pubmed]

A polygenic burden of rare disruptive mutations in schizophrenia
Purcell, Shaun M. et al., 2014 NATURE [Article] [Pubmed]

Exome sequencing identifies BRAF mutations in papillary craniopharyngiomas
Brastianos, Priscilla K. et al., 2014 NATURE GENETICS [Article] [Pubmed]

Landscape of genomic alterations in cervical carcinomas
Ojesina, Akinyemi I. et al., 2014 NATURE [Article] [Pubmed]

Simultaneous identification and prioritization of variants in familial, de novo, and somatic genetic disorders with VariantMaster
Santoni, Federico A. et al., 2014 GENOME RESEARCH [Article] [Pubmed]

Integrated genomic analysis identifies recurrent mutations and evolution patterns driving the initiation and progression of follicular lymphoma
Okosun, Jessica et al., 2014 NATURE GENETICS [Article] [Pubmed]

A novel method for detecting uniparental disomy from trio genotypes identifies a significant excess in children with developmental disorders
King, Daniel A. et al., 2014 GENOME RESEARCH [Article] [Pubmed]

Loss-of-function mutations in MICU1 cause a brain and muscle disorder linked to primary alterations in mitochondrial calcium signaling
Logan, Clare V. et al., 2014 NATURE GENETICS [Article] [Pubmed]

Upper Palaeolithic Siberian genome reveals dual ancestry of Native Americans
Raghavan, Maanasa et al., 2014 NATURE [Article] [Pubmed]

A large-scale screen for coding variants predisposing to psoriasis
Tang, Huayang et al., 2014 NATURE GENETICS [Article] [Pubmed]

Variation in chromatin accessibility in human kidney cancer links H3K36 methyltransferase loss with widespread RNA processing defects
Simon, Jeremy M. et al., 2014 GENOME RESEARCH [Article] [Pubmed]

The Landscape of Microsatellite Instability in Colorectal and Endometrial Cancer Genomes
Kim, Tae-Min et al., 2013 CELL [Article] [Pubmed]

ESR1 ligand-binding domain mutations in hormone-resistant breast cancer
Toy, Weiyi et al., 2013 NATURE GENETICS [Article] [Pubmed]

Somatic mutation of CDKN1B in small intestine neuroendocrine tumors
Francis, Joshua M. et al., 2013 NATURE GENETICS [Article] [Pubmed]

Whole-genome haplotype reconstruction using proximity-ligation and shotgun sequencing
Selvaraj, Siddarth et al., 2013 NATURE BIOTECHNOLOGY [Article] [Pubmed]

Development and validation of a clinical cancer genomic profiling test based on massively parallel DNA sequencing
Frampton, Garrett M. et al., 2013 NATURE BIOTECHNOLOGY [Article] [Pubmed]

Whole-genome and whole-exome sequencing of bladder cancer identifies frequent alterations in genes involved in sister chromatid cohesion and segregation
Guo, Guangwu et al., 2013 NATURE GENETICS [Article] [Pubmed]

Genome-wide evidence for speciation with gene flow in Heliconius butterflies
Martin, Simon H. et al., 2013 GENOME RESEARCH [Article] [Pubmed]

Estimating inbreeding coefficients from NGS data: Impact on genotype calling and allele frequency estimation
Vieira, Filipe G. et al., 2013 GENOME RESEARCH [Article] [Pubmed]

The haplotype-resolved genome and epigenome of the aneuploid HeLa cancer cell line
Adey, Andrew et al., 2013 NATURE [Article]

Genome Sequencing Reveals Loci under Artificial Selection that Underlie Disease Phenotypes in the Laboratory Rat
Atanur, Santosh S et al., 2013 CELL [Article]

Genotype calling and haplotyping in parent-offspring trios
Chen, Wei et al., 2013 GENOME RESEARCH [Article]

Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples
Cibulskis, Kristian et al., 2013 NATURE BIOTECHNOLOGY [Article]

SMIM1 underlies the Vel blood group and influences red blood cell traits
Cvejic, Ana et al., 2013 NATURE GENETICS [Article]

Assessing the phenotypic effects in the general population of rare variants in genes for a dominant Mendelian form of diabetes
Flannick, Jason et al., 2013 NATURE GENETICS [Article]

Mutations in GNAL cause primary torsion dystonia
Fuchs, Tania et al., 2013 NATURE GENETICS [Article]

TREM2 Variants in Alzheimer's Disease
Guerreiro, Rita et al., 2013 NEW ENGLAND JOURNAL OF MEDICINE [Article]

Read and assembly metrics inconsequential for clinical utility of whole-genome sequencing in mapping outbreaks
Harris, Simon R et al., 2013 NATURE BIOTECHNOLOGY [Article]

A rare nonsynonymous sequence variant in C3 is associated with high risk of age-related macular degeneration
Helgason, Hannes et al., 2013 NATURE GENETICS [Article]

Single molecule molecular inversion probes for targeted, high-accuracy detection of low-frequency variation
Hiatt, Joseph B et al., 2013 GENOME RESEARCH [Article]

The mutational landscape of adenoid cystic carcinoma
Ho, Allen S et al., 2013 NATURE GENETICS [Article]

Rare allelic forms of PRDM9 associated with childhood leukemogenesis
Hussin, Julie et al., 2013 GENOME RESEARCH [Article]

Next-generation sequencing of paired tyrosine kinase inhibitor-sensitive and -resistant EGFR mutant lung cancer cell lines identifies spectrum of DNA changes associated with drug resistance
Jia, Peilin et al., 2013 GENOME RESEARCH [Article]

The Next-Generation Sequencing Revolution and Its Impact on Genomics
Koboldt, Daniel C et al., 2013 CELL [Article]

Evolution and Impact of Subclonal Mutations in Chronic Lymphocytic Leukemia
Landau, Dan A et al., 2013 CELL [Article]

SOAPindel: Efficient identification of indels from short paired reads
Li, Shengting et al., 2013 GENOME RESEARCH [Article]

Massive genomic variation and strong selection in Arabidopsis thaliana lines from Sweden
Long, Quan et al., 2013 NATURE GENETICS [Article]

Exome sequencing identifies recurrent somatic mutations in EIF1AX and SF3B1 in uveal melanoma with disomy 3
Martin, Marcel et al., 2013 NATURE GENETICS [Article]

DREAMing of a patent-free human genome for clinical sequencing
McKernan, Kevin J et al., 2013 NATURE BIOTECHNOLOGY [Article]

Relapse-specific mutations in NT5C2 in childhood acute lymphoblastic leukemia
Meyer, Julia A et al., 2013 NATURE GENETICS [Article]

Non-invasive analysis of acquired resistance to cancer therapy by sequencing of plasma DNA
Murtaza, Muhammed et al., 2013 NATURE [Article]

Genome evolution during progression to breast cancer
Newburger, Daniel E et al., 2013 GENOME RESEARCH [Article]

Cell-type, allelic, and genetic signatures in the human pancreatic beta cell transcriptome
Nica, Alexandra C et al., 2013 GENOME RESEARCH [Article]

Maps of open chromatin highlight cell type-restricted patterns of regulatory sequence variation at hematological trait loci
Paul, Dirk S et al., 2013 GENOME RESEARCH [Article]

Mutations in TUBG1, DYNC1H1, KIF5C and KIF2A cause malformations of cortical development and microcephaly
Poirier, Karine et al., 2013 NATURE GENETICS [Article]

Great ape genetic diversity and population history
Prado-Martinez, Javier et al., 2013 NATURE [Article]

Desmoglein 1 deficiency results in severe dermatitis, multiple allergies and metabolic wasting
Samuelov, Liat et al., 2013 NATURE GENETICS [Article]

Genomic variation landscape of the human gut microbiome
Schloissnig, Siegfried et al., 2013 NATURE [Article]

Rare variants in CFI, C3 and C9 are associated with high risk of advanced age-related macular degeneration
Seddon, Johanna M et al., 2013 NATURE GENETICS [Article]

A recurrent germline PAX5 mutation confers susceptibility to pre-B cell acute lymphoblastic leukemia
Shah, Sohela et al., 2013 NATURE GENETICS [Article]

Genomic architecture of adaptive color pattern divergence and convergence in Heliconius butterflies
Supple, Megan A et al., 2013 GENOME RESEARCH [Article]

An integrative variant analysis pipeline for accurate genotype/haplotype inference in population NGS data
Wang, Yi et al., 2013 GENOME RESEARCH [Article]

An in-frame deletion at the polymerase active site of POLD1 causes a multisystem disorder with lipodystrophy
Weedon, Michael N et al., 2013 NATURE GENETICS [Article]

The draft genome of sweet orange (Citrus sinensis)
Xu, Qiang et al., 2013 NATURE GENETICS [Article]

Genetic programs in human and mouse early embryos revealed by single-cell RNA sequencing
Xue, Zhigang et al., 2013 NATURE [Article]

Comprehensive genome- and transcriptome-wide analyses of mutations associated with microsatellite instability in Korean gastric cancers
Yoon, Kwiyeom et al., 2013 GENOME RESEARCH [Article]

A heterozygous moth genome provides insights into herbivory and detoxification
You, Minsheng et al., 2013 NATURE GENETICS [Article]

Identification of a rare coding variant in complement 3 associated with age-related macular degeneration
Zhan, Xiaowei et al., 2013 NATURE GENETICS [Article]

TGFB2 mutations cause familial thoracic aortic aneurysms and dissections associated with mild systemic features of Marfan syndrome
Boileau, Catherine et al., 2012 NATURE GENETICS [Article]

Estimating the human mutation rate using autozygosity in a founder population
Campbell, Catarina D et al., 2012 NATURE GENETICS [Article]

Analysis of the Saccharomyces cerevisiae pan-genome reveals a pool of copy number variants distributed in diverse yeast strains from differing industrial environments
Dunn, Barbara et al., 2012 GENOME RESEARCH [Article]

Exome sequencing of extreme phenotypes identifies DCTN4 as a modifier of chronic Pseudomonas aeruginosa infection in cystic fibrosis
Emond, Mary J et al., 2012 NATURE GENETICS [Article]

Genome sequencing reveals complex speciation in the Drosophila simulans clade
Garrigan, Daniel et al., 2012 GENOME RESEARCH [Article]

Genomic Landscape of Non-Small Cell Lung Cancer in Smokers and Never-Smokers
Govindan, Ramaswamy et al., 2012 CELL [Article]

Recurrent mutations in the U2AF1 splicing factor in myelodysplastic syndromes
Graubert, Timothy A et al., 2012 NATURE GENETICS [Article]

Integrative analysis of genome-wide loss of heterozygosity and monoallelic expression at nucleotide resolution reveals disrupted pathways in triple-negative breast cancer
Ha, Gavin et al., 2012 GENOME RESEARCH [Article]

Prions are a common mechanism for phenotypic inheritance in wild yeasts
Halfmann, Randal et al., 2012 NATURE [Article]

Exome sequencing of hepatitis B virus-associated hepatocellular carcinoma
Huang, Jian et al., 2012 NATURE GENETICS [Article]

De novo assembly and genotyping of variants using colored de Bruijn graphs
Iqbal, Zamin et al., 2012 NATURE GENETICS [Article]

Genome-wide genetic changes during modern breeding of maize
Jiao, Yinping et al., 2012 NATURE GENETICS [Article]

Exome sequencing and the genetic basis of complex traits
Kiezun, Adam et al., 2012 NATURE GENETICS [Article]

Mutations in NMNAT1 cause Leber congenital amaurosis and identify a new disease pathway for retinal degeneration
Koenekoop, Robert K et al., 2012 NATURE GENETICS [Article]

Rate of de novo mutations and the importance of father's age to disease risk
Kong, Augustine et al., 2012 NATURE [Article]

Impaired intrinsic immunity to HSV-1 in human iPSC-derived TLR3-deficient CNS cells
Lafaille, Fabien G et al., 2012 NATURE [Article]

Genome mapping on nanochannel arrays for structural variation analysis and sequence assembly
Lam, Ernest T et al., 2012 NATURE BIOTECHNOLOGY [Article]

Detecting and annotating genetic variations using the HugeSeq pipeline
Lam, Hugo Y K et al., 2012 NATURE BIOTECHNOLOGY [Article]

Performance comparison of whole-genome sequencing platforms
Lam, Hugo Y K et al., 2012 NATURE BIOTECHNOLOGY [Article]

Mutations at a single codon in Mad homology 2 domain of SMAD4 cause Myhre syndrome
Le Goff, Carine et al., 2012 NATURE GENETICS [Article]

Mutation mapping and identification by whole-genome sequencing
Leshchiner, Ignaty et al., 2012 GENOME RESEARCH [Article]

A Systematic Survey of Loss-of-Function Variants in Human Protein-Coding Genes
MacArthur, Daniel G et al., 2012 SCIENCE [Article]

A High-Coverage Genome Sequence from an Archaic Denisovan Individual
Meyer, Matthias et al., 2012 SCIENCE [Article]

Whole-Genome Sequencing in Autism Identifies Hot Spots for De Novo Germline Mutation
Michaelson, Jacob J et al., 2012 CELL [Article]

Mutations in UVSSA cause UV-sensitive syndrome and impair RNA polymerase IIo processing in transcription-coupled nucleotide-excision repair
Nakazawa, Yuka et al., 2012 NATURE GENETICS [Article]

The malaria parasite Plasmodium vivax exhibits greater genetic diversity than Plasmodium falciparum
Neafsey, Daniel E et al., 2012 NATURE GENETICS [Article]

Patterns and rates of exonic de novo mutations in autism spectrum disorders
Neale, Benjamin M et al., 2012 NATURE [Article]

Extremely low-coverage sequencing and imputation increases power for genome-wide association studies
Pasaniuc, Bogdan et al., 2012 NATURE GENETICS [Article]

Comprehensive analysis of RNA-Seq data reveals extensive RNA editing in a human transcriptome
Peng, Zhiyu et al., 2012 NATURE BIOTECHNOLOGY [Article]

Comment on ``Widespread RNA and DNA Sequence Differences in the Human Transcriptome''
Pickrell, Joseph K et al., 2012 SCIENCE [Article]

Genome Sequencing of Pediatric Medulloblastoma Links Catastrophic DNA Rearrangements with TP53 Mutations
Rausch, Tobias et al., 2012 CELL [Article]

Optimized filtering reduces the error rate in detecting genomic variants by short-read sequencing
Reumers, Joke et al., 2012 NATURE BIOTECHNOLOGY [Article]

De novo germline and postzygotic mutations in AKT3, PIK3R2 and PIK3CA cause a spectrum of related megalencephaly syndromes
Riviere, Jean-Baptiste et al., 2012 NATURE GENETICS [Article]

De novo mutations in the actin genes ACTB and ACTG1 cause Baraitser-Winter syndrome
Riviere, Jean-Baptiste et al., 2012 NATURE GENETICS [Article]

Comprehensive genomic analysis identifies SOX2 as a frequently amplified gene in small-cell lung cancer
Rudin, Charles M et al., 2012 NATURE GENETICS [Article]

Mutations in SWI/SNF chromatin remodeling complex gene ARID1B cause Coffin-Siris syndrome
Santen, Gijs W E et al., 2012 NATURE GENETICS [Article]

Recurrent R-spondin fusions in colon cancer
Seshagiri, Somasekar et al., 2012 NATURE [Article]

Efficient de novo assembly of large genomes using compressed data structures
Simpson, Jared T et al., 2012 GENOME RESEARCH [Article]

Joint genotyping on the fly: Identifying variation among a sequenced panel of inbred lines
Stone, Eric A et al., 2012 GENOME RESEARCH [Article]

Whole genome sequencing of matched primary and metastatic acral melanomas
Turajlic, Samra et al., 2012 GENOME RESEARCH [Article]

Heterozygous missense mutations in SMARCA2 cause Nicolaides-Baraitser syndrome
Van Houdt, Jeroen K J et al., 2012 NATURE GENETICS [Article]

Mutations in the RNA exosome component gene EXOSC3 cause pontocerebellar hypoplasia and spinal motor neuron degeneration
Wan, Jijun et al., 2012 NATURE GENETICS [Article]

Interpreting noncoding genetic variation in complex traits and human disease
Ward, Lucas D et al., 2012 NATURE BIOTECHNOLOGY [Article]

ISPD loss-of-function mutations disrupt dystroglycan O-mannosylation and cause Walker-Warburg syndrome
Willer, Tobias et al., 2012 NATURE GENETICS [Article]

Exome sequencing of gastric adenocarcinoma identifies recurrent somatic mutations in cell adhesion and chromatin remodeling genes
Zang, Zhi Jiang et al., 2012 NATURE GENETICS [Article]

Exome sequencing identifies MVK mutations in disseminated superficial actinic porokeratosis
Zhang, Sheng-Quan et al., 2012 NATURE GENETICS [Article]

Seventy-five genetic loci influencing the human red blood cell
van der Harst, Pim et al., 2012 NATURE [Article]

Accurate and comprehensive sequencing of personal genomes
Ajay, Subramanian S et al., 2011 GENOME RESEARCH [Article]

Exome sequencing identifies truncating mutations in PRRT2 that cause paroxysmal kinesigenic dyskinesia
Chen, Wan-Jin et al., 2011 NATURE GENETICS [Article]

Performance comparison of exome DNA sequencing technologies
Clark, Michael J et al., 2011 NATURE BIOTECHNOLOGY [Article]

Bayesian inference of ancient human demography from individual genome sequences
Gronau, Ilan et al., 2011 NATURE GENETICS [Article]

Frequent mutations of chromatin remodeling genes in transitional cell carcinoma of the bladder
Gui, Yaoting et al., 2011 NATURE GENETICS [Article]

Haplotype-resolved genome sequencing of a Gujarati Indian individual
Kitzman, Jacob O et al., 2011 NATURE BIOTECHNOLOGY [Article]

SNP detection and genotyping from low-coverage sequencing data on multiple diploid samples
Le, Si Quang et al., 2011 GENOME RESEARCH [Article]

Inference of human population history from individual whole-genome sequences
Li, Heng et al., 2011 NATURE [Article]

Low-coverage sequencing: Implications for design of complex trait association studies
Li, Yun et al., 2011 GENOME RESEARCH [Article]

The Human Mitochondrial Transcriptome
Mercer, Tim R et al., 2011 CELL [Article]

A rare penetrant mutation in CFH confers high risk of age-related macular degeneration
Raychaudhuri, Soumya et al., 2011 NATURE GENETICS [Article]

Mapping Rare and Common Causal Alleles for Complex Human Diseases
Raychaudhuri, Soumya et al., 2011 CELL [Article]

Copy number and targeted mutational analysis reveals novel somatic events in metastatic prostate tumors
Robbins, Christiane M et al., 2011 GENOME RESEARCH [Article]

Comparing strategies to fine-map the association of common SNPs at chromosome 9p21 with type 2 diabetes and myocardial infarction
Shea, Jessica et al., 2011 NATURE GENETICS [Article]

SF3B1 and Other Novel Cancer Genes in Chronic Lymphocytic Leukemia
Wang, Lili et al., 2011 NEW ENGLAND JOURNAL OF MEDICINE [Article]

Putting epigenome comparison into practice
Milosavljevic, Aleksandar et al., 2010 NATURE BIOTECHNOLOGY [Article]


et al., [Article]

We use RSS feeds to update our list of citations weekly. You can use the feeds yourself if you'd like to get notified when a new article comes out citing GATK in one of the journals we track. There is a separate feed for each of our papers; papers for which there is no feed available are not shown.



2 New citations this week:


Discovery of a new repeat family in the Callithrix jacchus genome
Konkel, Miriam K. et al., 2016 GENOME RESEARCH [Article] [Pubmed]

Genetic predisposition for beta cell fragility underlies type 1 and type 2 diabetes
Dooley, James et al., 2016 NATURE GENETICS [Article] [Pubmed]

The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data
McKenna A et al., 2010 GENOME RESEARCH [Article] [Pubmed]


2 New citations this week:


Discovery of a new repeat family in the Callithrix jacchus genome
Konkel, Miriam K. et al., 2016 GENOME RESEARCH [Article] [Pubmed]

Genetic predisposition for beta cell fragility underlies type 1 and type 2 diabetes
Dooley, James et al., 2016 NATURE GENETICS [Article] [Pubmed]

A framework for variation discovery and genotyping using next-generation DNA sequencing data
DePristo M et al., 2011 NATURE GENETICS [Article] [Pubmed]


No new citations this week.


 

Browse the citations list by year of publication.


Genomic analysis identifies new drivers and progression pathways in skin basal cell carcinoma
Bonilla, Ximena et al., 2016 NATURE GENETICS [Article] [Pubmed]

Inactivating Variants in ANGPTL4 and Risk of Coronary Artery Disease
Dewey, Frederick F. et al., 2016 NEW ENGLAND JOURNAL OF MEDICINE [Article] [Pubmed]

Frequent somatic CDH1 loss-of-function mutations in plasmacytoid variant bladder cancer
Al-Ahmadie, Hikmat A. et al., 2016 NATURE GENETICS [Article] [Pubmed]

Ancient gene flow from early modern humans into Eastern Neanderthals
Kuhlwilm, Martin et al., 2016 NATURE [Article] [Pubmed]

Haplotyping germline and cancer genomes with high-throughput linked-read sequencing
Zheng, Grace X. Y. et al., 2016 NATURE BIOTECHNOLOGY [Article] [Pubmed]

Divergent clonal selection dominates medulloblastoma at recurrence
Morrissy, A. Sorana et al., 2016 NATURE [Article] [Pubmed]

Structural genomic changes underlie alternative reproductive strategies in the ruff (Philomachus pugnax)
Lamichhaney, Sangeet et al., 2016 NATURE GENETICS [Article] [Pubmed]

The genomic landscape of juvenile myelomonocytic leukemia
Stieglitz, Elliot et al., 2015 NATURE GENETICS [Article] [Pubmed]

Alternative transcription initiation leads to expression of a novel ALK isoform in cancer
Wiesner, Thomas et al., 2015 NATURE [Article] [Pubmed]

The genome of the vervet (Chlorocebus aethiops sabaeus)
Warren, Wesley C. et al., 2015 GENOME RESEARCH [Article] [Pubmed]

BET inhibitor resistance emerges from leukaemia stem cells
Fong, Chun Yew et al., 2015 NATURE [Article] [Pubmed]

Linked selection and recombination rate variation drive the evolution of the genomic landscape of differentiation across the speciation continuum of Ficedula flycatchers
Burri, Reto et al., 2015 GENOME RESEARCH [Article] [Pubmed]

Tandem repeat variation in human and great ape populations and its impact on gene expression divergence
Sonay, Tugce Bilgin et al., 2015 GENOME RESEARCH [Article] [Pubmed]

Extensive de novo mutation rate variation between individuals and across the genome of Chlamydomonas reinhardtii
Ness, Rob W. et al., 2015 GENOME RESEARCH [Article] [Pubmed]

Genomic analysis of mycosis fungoides and Sezary syndrome identifies recurrent alterations in TNFR2
Ungewickell, Alexander et al., 2015 NATURE GENETICS [Article] [Pubmed]

The use of exome capture RNA-seq for highly degraded RNA with application to clinical cancer sequencing
Cieslik, Marcin et al., 2015 GENOME RESEARCH [Article] [Pubmed]

Genomics and drug profiling of fatal TCF3-HLF-positive acute lymphoblastic leukemia identifies recurrent mutation patterns and therapeutic options
Fischer, Ute et al., 2015 NATURE GENETICS [Article] [Pubmed]

Chimeric EWSR1-FLI1 regulates the Ewing sarcoma susceptibility gene EGR2 via a GGAA microsatellite
Gruenewald, Thomas G. P. et al., 2015 NATURE GENETICS [Article] [Pubmed]

Lanosterol reverses protein aggregation in cataracts
Zhao, Ling et al., 2015 NATURE [Article] [Pubmed]

Genetic evidence for two founding populations of the Americas
Skoglund, Pontus et al., 2015 NATURE [Article] [Pubmed]

Exome sequencing identifies somatic mutations of DDX3X in natural killer/T-cell lymphoma
Jiang, Lu et al., 2015 NATURE GENETICS [Article] [Pubmed]

Parent-progeny sequencing indicates higher mutation rates in heterozygotes
Yang, Sihai et al., 2015 NATURE [Article] [Pubmed]

Sparse whole-genome sequencing identifies two loci for major depressive disorder
Cai, Na et al., 2015 NATURE [Article] [Pubmed]

Germline mutation rates and the long-term phenotypic effects of mutation accumulation in wild-type laboratory mice and mutator mice
Uchimura, Arikuni et al., 2015 GENOME RESEARCH [Article] [Pubmed]

Relapsed neuroblastomas show frequent RAS-MAPK pathway mutations
Eleveld, Thomas F. et al., 2015 NATURE GENETICS [Article] [Pubmed]

Rare A2ML1 variants confer susceptibility to otitis media
Santos-Cortez, Regie Lyn P. et al., 2015 NATURE GENETICS [Article] [Pubmed]

Loss-of-function variants in ATM confer risk of gastric cancer
Helgason, Hannes et al., 2015 NATURE GENETICS [Article] [Pubmed]

Massively parallel quantification of the regulatory effects of noncoding genetic variation in a human cohort
Vockley, Christopher M. et al., 2015 GENOME RESEARCH [Article] [Pubmed]

Whole-genome characterization of chemoresistant ovarian cancer
Patch, Ann-Marie et al., 2015 NATURE [Article] [Pubmed]

Comprehensive models of human primary and metastatic colorectal tumors in immunodeficient and immunocompetent mice by chemokine targeting
Chen, Huanhuan Joyce et al., 2015 NATURE BIOTECHNOLOGY [Article] [Pubmed]

De novo assembly of a haplotype-resolved human genome
Cao, Hongzhi et al., 2015 NATURE BIOTECHNOLOGY [Article] [Pubmed]

Prospective Derivation of a Living Organoid Biobank of Colorectal Cancer Patients
van de Wetering, Marc et al., 2015 CELL [Article] [Pubmed]

Sequential cancer mutations in cultured human intestinal stem cells
Drost, Jarno et al., 2015 NATURE [Article] [Pubmed]

Biallelic mutations in SNX14 cause a syndromic form of cerebellar atrophy and lysosome-autophagosome dysfunction
Akizu, Naiara et al., 2015 NATURE GENETICS [Article] [Pubmed]

Loss of delta-catenin function in severe autism
Turner, Tychele N. et al., 2015 NATURE [Article] [Pubmed]

The Paf1 complex represses small-RNA-mediated epigenetic gene silencing
Kowalik, Katarzyna Maria et al., 2015 NATURE [Article] [Pubmed]

Large-scale whole-genome sequencing of the Icelandic population
Gudbjartsson, Daniel F. et al., 2015 NATURE GENETICS [Article] [Pubmed]

Germline mutations in ETV6 are associated with thrombocytopenia, red cell macrocytosis and predisposition to lymphoblastic leukemia
Noetzli, Leila et al., 2015 NATURE GENETICS [Article] [Pubmed]

Quality score compression improves genotyping accuracy
Yu, Y. William et al., 2015 NATURE BIOTECHNOLOGY [Article] [Pubmed]

Polyploidy can drive rapid adaptation in yeast
Selmecki, Anna M. et al., 2015 NATURE [Article] [Pubmed]

Germline gain-of-function mutations in AFF4 cause a developmental syndrome functionally linking the super elongation complex and cohesin
Izumi, Kosuke et al., 2015 NATURE GENETICS [Article] [Pubmed]

Stromal gene expression defines poor-prognosis subtypes in colorectal cancer
Calon, Alexandre et al., 2015 NATURE GENETICS [Article] [Pubmed]

The genomic and phenotypic diversity of Schizosaccharomyces pombe
Jeffares, Daniel C. et al., 2015 NATURE GENETICS [Article] [Pubmed]

Whole-genome and multisector exome sequencing of primary and post-treatment glioblastoma reveals patterns of tumor evolution
Kim, Hoon et al., 2015 GENOME RESEARCH [Article] [Pubmed]

Resequencing 302 wild and cultivated accessions identifies genes related to domestication and improvement in soybean
Zhou, Zhengkui et al., 2015 NATURE BIOTECHNOLOGY [Article] [Pubmed]

Combined hereditary and somatic mutations of replication error repair genes result in rapid onset of ultra-hypermutated cancers
Shlien, Adam et al., 2015 NATURE GENETICS [Article] [Pubmed]

Adaptation and possible ancient interspecies introgression in pigs identified by whole-genome sequencing
Ai, Huashui et al., 2015 NATURE GENETICS [Article] [Pubmed]

Large multiallelic copy number variations in humans
Handsaker, Robert E. et al., 2015 NATURE GENETICS [Article] [Pubmed]

Genetic and phenotypic intra-species variation in Candida albicans
Hirakawa, Matthew P. et al., 2015 GENOME RESEARCH [Article] [Pubmed]

Exome sequencing identifies rare LDLR and APOA5 alleles conferring risk for myocardial infarction
Do, Ron et al., 2015 NATURE [Article] [Pubmed]

Convergent loss of PTEN leads to clinical resistance to a PI(3)K alpha inhibitor
Juric, Dejan et al., 2015 NATURE [Article] [Pubmed]

Spectrum of diverse genomic alterations define non-clear cell renal carcinoma
Durinck, Steffen et al., 2015 NATURE GENETICS [Article] [Pubmed]

Convergent evolution and adaptation of Pseudomonas aeruginosa within patients with cystic fibrosis
Marvig, Rasmus Lykke et al., 2015 NATURE GENETICS [Article] [Pubmed]

A recurrent de novo mutation in KCNC1 causes progressive myoclonus epilepsy
Muona, Mikko et al., 2015 NATURE GENETICS [Article] [Pubmed]

The mutational landscapes of genetic and chemical models of Kras-driven lung cancer
Westcott, Peter M. K. et al., 2015 NATURE [Article] [Pubmed]

A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping
Rao, Suhas S. P. et al., 2014 CELL [Article] [Pubmed]

Predicting immunogenic tumour mutations by combining mass spectrometry and exome sequencing
Yadav, Mahesh et al., 2014 NATURE [Article] [Pubmed]

The contribution of de novo coding mutations to autism spectrum disorder
Iossifov, Ivan et al., 2014 NATURE [Article] [Pubmed]

Synaptic, transcriptional and chromatin genes disrupted in autism
De Rubeis, Silvia et al., 2014 NATURE [Article] [Pubmed]

Rapid modelling of cooperating genetic events in cancer through somatic genome editing
Sanchez-Rivera, Francisco J. et al., 2014 NATURE [Article] [Pubmed]

Estimating genotype error rates from high-coverage next-generation sequence data
Wall, Jeffrey D. et al., 2014 GENOME RESEARCH [Article] [Pubmed]

Large-scale identification of chemically induced mutations in Drosophila melanogaster
Haelterman, Nele A. et al., 2014 GENOME RESEARCH [Article] [Pubmed]

Ancient human genomes suggest three ancestral populations for present-day Europeans
Lazaridis, Iosif et al., 2014 NATURE [Article] [Pubmed]

Multi-platform assessment of transcriptome profiling using RNA-seq in the ABRF next-generation sequencing study
Li, Sheng et al., 2014 NATURE BIOTECHNOLOGY [Article] [Pubmed]

Clonal evolution in breast cancer revealed by single nucleus genome sequencing
Wang, Yong et al., 2014 NATURE [Article] [Pubmed]

A common Greenlandic TBC1D4 variant confers muscle insulin resistance and type 2 diabetes
Moltke, Ida et al., 2014 NATURE [Article] [Pubmed]

Integrating mapping-, assembly- and haplotype-based approaches for calling variants in clinical sequencing applications
Rimmer, Andy et al., 2014 NATURE GENETICS [Article] [Pubmed]

Whole-genome sequence variation, population structure and demographic history of the Dutch population
Francioli, Laurent C. et al., 2014 NATURE GENETICS [Article] [Pubmed]

Population genomics of parallel hybrid zones in the mimetic butterflies, H. melpomene and H. erato
Nadeau, Nicola J. et al., 2014 GENOME RESEARCH [Article] [Pubmed]

CLP1 Founder Mutation Links tRNA Splicing and Maturation to Cerebellar Development and Neurodegeneration
Schaffer, Ashleigh E. et al., 2014 CELL [Article] [Pubmed]

Somatic mutations found in the healthy blood compartment of a 115-yr-old woman demonstrate oligoclonal hematopoiesis
Holstege, Henne et al., 2014 GENOME RESEARCH [Article] [Pubmed]

Domains of genome-wide gene expression dysregulation in Down's syndrome
Letourneau, Audrey et al., 2014 NATURE [Article] [Pubmed]

Identification of genomic alterations in oesophageal squamous cell cancer
Song, Yongmei et al., 2014 NATURE [Article] [Pubmed]

Mutations in TJP2 cause progressive cholestatic liver disease
Sambrotta, Melissa et al., 2014 NATURE GENETICS [Article] [Pubmed]

doublesex is a mimicry supergene
Kunte, K. et al., 2014 NATURE [Article] [Pubmed]

A recurrent inactivating mutation in RHOA GTPase in angioimmunoblastic T cell lymphoma
Yoo, Hae Yong et al., 2014 NATURE GENETICS [Article] [Pubmed]

A cascade of DNA-binding proteins for sexual commitment and development in Plasmodium
Sinha, Abhinav et al., 2014 NATURE [Article] [Pubmed]

Integrating human sequence data sets provides a resource of benchmark SNP and indel genotype calls
Zook, Justin M. et al., 2014 NATURE BIOTECHNOLOGY [Article] [Pubmed]

Evolution and transmission of drug-resistant tuberculosis in a Russian population
Casali, Nicola et al., 2014 NATURE GENETICS [Article] [Pubmed]

Derived immune and ancestral pigmentation alleles in a 7,000-year-old Mesolithic European
Olalde, Inigo et al., 2014 NATURE [Article] [Pubmed]

A polygenic burden of rare disruptive mutations in schizophrenia
Purcell, Shaun M. et al., 2014 NATURE [Article] [Pubmed]

Exome sequencing identifies BRAF mutations in papillary craniopharyngiomas
Brastianos, Priscilla K. et al., 2014 NATURE GENETICS [Article] [Pubmed]

Landscape of genomic alterations in cervical carcinomas
Ojesina, Akinyemi I. et al., 2014 NATURE [Article] [Pubmed]

Simultaneous identification and prioritization of variants in familial, de novo, and somatic genetic disorders with VariantMaster
Santoni, Federico A. et al., 2014 GENOME RESEARCH [Article] [Pubmed]

Integrated genomic analysis identifies recurrent mutations and evolution patterns driving the initiation and progression of follicular lymphoma
Okosun, Jessica et al., 2014 NATURE GENETICS [Article] [Pubmed]

A novel method for detecting uniparental disomy from trio genotypes identifies a significant excess in children with developmental disorders
King, Daniel A. et al., 2014 GENOME RESEARCH [Article] [Pubmed]

Loss-of-function mutations in MICU1 cause a brain and muscle disorder linked to primary alterations in mitochondrial calcium signaling
Logan, Clare V. et al., 2014 NATURE GENETICS [Article] [Pubmed]

Upper Palaeolithic Siberian genome reveals dual ancestry of Native Americans
Raghavan, Maanasa et al., 2014 NATURE [Article] [Pubmed]

A large-scale screen for coding variants predisposing to psoriasis
Tang, Huayang et al., 2014 NATURE GENETICS [Article] [Pubmed]

Variation in chromatin accessibility in human kidney cancer links H3K36 methyltransferase loss with widespread RNA processing defects
Simon, Jeremy M. et al., 2014 GENOME RESEARCH [Article] [Pubmed]

The Landscape of Microsatellite Instability in Colorectal and Endometrial Cancer Genomes
Kim, Tae-Min et al., 2013 CELL [Article] [Pubmed]

ESR1 ligand-binding domain mutations in hormone-resistant breast cancer
Toy, Weiyi et al., 2013 NATURE GENETICS [Article] [Pubmed]

Somatic mutation of CDKN1B in small intestine neuroendocrine tumors
Francis, Joshua M. et al., 2013 NATURE GENETICS [Article] [Pubmed]

Whole-genome haplotype reconstruction using proximity-ligation and shotgun sequencing
Selvaraj, Siddarth et al., 2013 NATURE BIOTECHNOLOGY [Article] [Pubmed]

Development and validation of a clinical cancer genomic profiling test based on massively parallel DNA sequencing
Frampton, Garrett M. et al., 2013 NATURE BIOTECHNOLOGY [Article] [Pubmed]

Whole-genome and whole-exome sequencing of bladder cancer identifies frequent alterations in genes involved in sister chromatid cohesion and segregation
Guo, Guangwu et al., 2013 NATURE GENETICS [Article] [Pubmed]

Genome-wide evidence for speciation with gene flow in Heliconius butterflies
Martin, Simon H. et al., 2013 GENOME RESEARCH [Article] [Pubmed]

Estimating inbreeding coefficients from NGS data: Impact on genotype calling and allele frequency estimation
Vieira, Filipe G. et al., 2013 GENOME RESEARCH [Article] [Pubmed]

The haplotype-resolved genome and epigenome of the aneuploid HeLa cancer cell line
Adey, Andrew et al., 2013 NATURE [Article]

Genome Sequencing Reveals Loci under Artificial Selection that Underlie Disease Phenotypes in the Laboratory Rat
Atanur, Santosh S et al., 2013 CELL [Article]

Genotype calling and haplotyping in parent-offspring trios
Chen, Wei et al., 2013 GENOME RESEARCH [Article]

Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples
Cibulskis, Kristian et al., 2013 NATURE BIOTECHNOLOGY [Article]

SMIM1 underlies the Vel blood group and influences red blood cell traits
Cvejic, Ana et al., 2013 NATURE GENETICS [Article]

Assessing the phenotypic effects in the general population of rare variants in genes for a dominant Mendelian form of diabetes
Flannick, Jason et al., 2013 NATURE GENETICS [Article]

Mutations in GNAL cause primary torsion dystonia
Fuchs, Tania et al., 2013 NATURE GENETICS [Article]

TREM2 Variants in Alzheimer's Disease
Guerreiro, Rita et al., 2013 NEW ENGLAND JOURNAL OF MEDICINE [Article]

Read and assembly metrics inconsequential for clinical utility of whole-genome sequencing in mapping outbreaks
Harris, Simon R et al., 2013 NATURE BIOTECHNOLOGY [Article]

A rare nonsynonymous sequence variant in C3 is associated with high risk of age-related macular degeneration
Helgason, Hannes et al., 2013 NATURE GENETICS [Article]

Single molecule molecular inversion probes for targeted, high-accuracy detection of low-frequency variation
Hiatt, Joseph B et al., 2013 GENOME RESEARCH [Article]

The mutational landscape of adenoid cystic carcinoma
Ho, Allen S et al., 2013 NATURE GENETICS [Article]

Rare allelic forms of PRDM9 associated with childhood leukemogenesis
Hussin, Julie et al., 2013 GENOME RESEARCH [Article]

Next-generation sequencing of paired tyrosine kinase inhibitor-sensitive and -resistant EGFR mutant lung cancer cell lines identifies spectrum of DNA changes associated with drug resistance
Jia, Peilin et al., 2013 GENOME RESEARCH [Article]

The Next-Generation Sequencing Revolution and Its Impact on Genomics
Koboldt, Daniel C et al., 2013 CELL [Article]

Evolution and Impact of Subclonal Mutations in Chronic Lymphocytic Leukemia
Landau, Dan A et al., 2013 CELL [Article]

SOAPindel: Efficient identification of indels from short paired reads
Li, Shengting et al., 2013 GENOME RESEARCH [Article]

Massive genomic variation and strong selection in Arabidopsis thaliana lines from Sweden
Long, Quan et al., 2013 NATURE GENETICS [Article]

Exome sequencing identifies recurrent somatic mutations in EIF1AX and SF3B1 in uveal melanoma with disomy 3
Martin, Marcel et al., 2013 NATURE GENETICS [Article]

DREAMing of a patent-free human genome for clinical sequencing
McKernan, Kevin J et al., 2013 NATURE BIOTECHNOLOGY [Article]

Relapse-specific mutations in NT5C2 in childhood acute lymphoblastic leukemia
Meyer, Julia A et al., 2013 NATURE GENETICS [Article]

Non-invasive analysis of acquired resistance to cancer therapy by sequencing of plasma DNA
Murtaza, Muhammed et al., 2013 NATURE [Article]

Genome evolution during progression to breast cancer
Newburger, Daniel E et al., 2013 GENOME RESEARCH [Article]

Cell-type, allelic, and genetic signatures in the human pancreatic beta cell transcriptome
Nica, Alexandra C et al., 2013 GENOME RESEARCH [Article]

Maps of open chromatin highlight cell type-restricted patterns of regulatory sequence variation at hematological trait loci
Paul, Dirk S et al., 2013 GENOME RESEARCH [Article]

Mutations in TUBG1, DYNC1H1, KIF5C and KIF2A cause malformations of cortical development and microcephaly
Poirier, Karine et al., 2013 NATURE GENETICS [Article]

Great ape genetic diversity and population history
Prado-Martinez, Javier et al., 2013 NATURE [Article]

Desmoglein 1 deficiency results in severe dermatitis, multiple allergies and metabolic wasting
Samuelov, Liat et al., 2013 NATURE GENETICS [Article]

Genomic variation landscape of the human gut microbiome
Schloissnig, Siegfried et al., 2013 NATURE [Article]

Rare variants in CFI, C3 and C9 are associated with high risk of advanced age-related macular degeneration
Seddon, Johanna M et al., 2013 NATURE GENETICS [Article]

A recurrent germline PAX5 mutation confers susceptibility to pre-B cell acute lymphoblastic leukemia
Shah, Sohela et al., 2013 NATURE GENETICS [Article]

Genomic architecture of adaptive color pattern divergence and convergence in Heliconius butterflies
Supple, Megan A et al., 2013 GENOME RESEARCH [Article]

An integrative variant analysis pipeline for accurate genotype/haplotype inference in population NGS data
Wang, Yi et al., 2013 GENOME RESEARCH [Article]

An in-frame deletion at the polymerase active site of POLD1 causes a multisystem disorder with lipodystrophy
Weedon, Michael N et al., 2013 NATURE GENETICS [Article]

The draft genome of sweet orange (Citrus sinensis)
Xu, Qiang et al., 2013 NATURE GENETICS [Article]

Genetic programs in human and mouse early embryos revealed by single-cell RNA sequencing
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Integrating mapping-, assembly- and haplotype-based approaches for calling variants in clinical sequencing applications
Rimmer, Andy et al., 2014 NATURE GENETICS [Article] [Pubmed]

Whole-genome sequence variation, population structure and demographic history of the Dutch population
Francioli, Laurent C. et al., 2014 NATURE GENETICS [Article] [Pubmed]

Mutations in TJP2 cause progressive cholestatic liver disease
Sambrotta, Melissa et al., 2014 NATURE GENETICS [Article] [Pubmed]

A recurrent inactivating mutation in RHOA GTPase in angioimmunoblastic T cell lymphoma
Yoo, Hae Yong et al., 2014 NATURE GENETICS [Article] [Pubmed]

Evolution and transmission of drug-resistant tuberculosis in a Russian population
Casali, Nicola et al., 2014 NATURE GENETICS [Article] [Pubmed]

Exome sequencing identifies BRAF mutations in papillary craniopharyngiomas
Brastianos, Priscilla K. et al., 2014 NATURE GENETICS [Article] [Pubmed]

Integrated genomic analysis identifies recurrent mutations and evolution patterns driving the initiation and progression of follicular lymphoma
Okosun, Jessica et al., 2014 NATURE GENETICS [Article] [Pubmed]

Loss-of-function mutations in MICU1 cause a brain and muscle disorder linked to primary alterations in mitochondrial calcium signaling
Logan, Clare V. et al., 2014 NATURE GENETICS [Article] [Pubmed]

A large-scale screen for coding variants predisposing to psoriasis
Tang, Huayang et al., 2014 NATURE GENETICS [Article] [Pubmed]

ESR1 ligand-binding domain mutations in hormone-resistant breast cancer
Toy, Weiyi et al., 2013 NATURE GENETICS [Article] [Pubmed]

Somatic mutation of CDKN1B in small intestine neuroendocrine tumors
Francis, Joshua M. et al., 2013 NATURE GENETICS [Article] [Pubmed]

Whole-genome and whole-exome sequencing of bladder cancer identifies frequent alterations in genes involved in sister chromatid cohesion and segregation
Guo, Guangwu et al., 2013 NATURE GENETICS [Article] [Pubmed]

SMIM1 underlies the Vel blood group and influences red blood cell traits
Cvejic, Ana et al., 2013 NATURE GENETICS [Article]

Assessing the phenotypic effects in the general population of rare variants in genes for a dominant Mendelian form of diabetes
Flannick, Jason et al., 2013 NATURE GENETICS [Article]

Mutations in GNAL cause primary torsion dystonia
Fuchs, Tania et al., 2013 NATURE GENETICS [Article]

A rare nonsynonymous sequence variant in C3 is associated with high risk of age-related macular degeneration
Helgason, Hannes et al., 2013 NATURE GENETICS [Article]

The mutational landscape of adenoid cystic carcinoma
Ho, Allen S et al., 2013 NATURE GENETICS [Article]

Massive genomic variation and strong selection in Arabidopsis thaliana lines from Sweden
Long, Quan et al., 2013 NATURE GENETICS [Article]

Exome sequencing identifies recurrent somatic mutations in EIF1AX and SF3B1 in uveal melanoma with disomy 3
Martin, Marcel et al., 2013 NATURE GENETICS [Article]

Relapse-specific mutations in NT5C2 in childhood acute lymphoblastic leukemia
Meyer, Julia A et al., 2013 NATURE GENETICS [Article]

Mutations in TUBG1, DYNC1H1, KIF5C and KIF2A cause malformations of cortical development and microcephaly
Poirier, Karine et al., 2013 NATURE GENETICS [Article]

Desmoglein 1 deficiency results in severe dermatitis, multiple allergies and metabolic wasting
Samuelov, Liat et al., 2013 NATURE GENETICS [Article]

Rare variants in CFI, C3 and C9 are associated with high risk of advanced age-related macular degeneration
Seddon, Johanna M et al., 2013 NATURE GENETICS [Article]

A recurrent germline PAX5 mutation confers susceptibility to pre-B cell acute lymphoblastic leukemia
Shah, Sohela et al., 2013 NATURE GENETICS [Article]

An in-frame deletion at the polymerase active site of POLD1 causes a multisystem disorder with lipodystrophy
Weedon, Michael N et al., 2013 NATURE GENETICS [Article]

The draft genome of sweet orange (Citrus sinensis)
Xu, Qiang et al., 2013 NATURE GENETICS [Article]

A heterozygous moth genome provides insights into herbivory and detoxification
You, Minsheng et al., 2013 NATURE GENETICS [Article]

Identification of a rare coding variant in complement 3 associated with age-related macular degeneration
Zhan, Xiaowei et al., 2013 NATURE GENETICS [Article]

TGFB2 mutations cause familial thoracic aortic aneurysms and dissections associated with mild systemic features of Marfan syndrome
Boileau, Catherine et al., 2012 NATURE GENETICS [Article]

Estimating the human mutation rate using autozygosity in a founder population
Campbell, Catarina D et al., 2012 NATURE GENETICS [Article]

Exome sequencing of extreme phenotypes identifies DCTN4 as a modifier of chronic Pseudomonas aeruginosa infection in cystic fibrosis
Emond, Mary J et al., 2012 NATURE GENETICS [Article]

Recurrent mutations in the U2AF1 splicing factor in myelodysplastic syndromes
Graubert, Timothy A et al., 2012 NATURE GENETICS [Article]

Exome sequencing of hepatitis B virus-associated hepatocellular carcinoma
Huang, Jian et al., 2012 NATURE GENETICS [Article]

De novo assembly and genotyping of variants using colored de Bruijn graphs
Iqbal, Zamin et al., 2012 NATURE GENETICS [Article]

Genome-wide genetic changes during modern breeding of maize
Jiao, Yinping et al., 2012 NATURE GENETICS [Article]

Exome sequencing and the genetic basis of complex traits
Kiezun, Adam et al., 2012 NATURE GENETICS [Article]

Mutations in NMNAT1 cause Leber congenital amaurosis and identify a new disease pathway for retinal degeneration
Koenekoop, Robert K et al., 2012 NATURE GENETICS [Article]

Mutations at a single codon in Mad homology 2 domain of SMAD4 cause Myhre syndrome
Le Goff, Carine et al., 2012 NATURE GENETICS [Article]

Mutations in UVSSA cause UV-sensitive syndrome and impair RNA polymerase IIo processing in transcription-coupled nucleotide-excision repair
Nakazawa, Yuka et al., 2012 NATURE GENETICS [Article]

The malaria parasite Plasmodium vivax exhibits greater genetic diversity than Plasmodium falciparum
Neafsey, Daniel E et al., 2012 NATURE GENETICS [Article]

Extremely low-coverage sequencing and imputation increases power for genome-wide association studies
Pasaniuc, Bogdan et al., 2012 NATURE GENETICS [Article]

De novo germline and postzygotic mutations in AKT3, PIK3R2 and PIK3CA cause a spectrum of related megalencephaly syndromes
Riviere, Jean-Baptiste et al., 2012 NATURE GENETICS [Article]

De novo mutations in the actin genes ACTB and ACTG1 cause Baraitser-Winter syndrome
Riviere, Jean-Baptiste et al., 2012 NATURE GENETICS [Article]

Comprehensive genomic analysis identifies SOX2 as a frequently amplified gene in small-cell lung cancer
Rudin, Charles M et al., 2012 NATURE GENETICS [Article]

Mutations in SWI/SNF chromatin remodeling complex gene ARID1B cause Coffin-Siris syndrome
Santen, Gijs W E et al., 2012 NATURE GENETICS [Article]

Heterozygous missense mutations in SMARCA2 cause Nicolaides-Baraitser syndrome
Van Houdt, Jeroen K J et al., 2012 NATURE GENETICS [Article]

Mutations in the RNA exosome component gene EXOSC3 cause pontocerebellar hypoplasia and spinal motor neuron degeneration
Wan, Jijun et al., 2012 NATURE GENETICS [Article]

ISPD loss-of-function mutations disrupt dystroglycan O-mannosylation and cause Walker-Warburg syndrome
Willer, Tobias et al., 2012 NATURE GENETICS [Article]

Exome sequencing of gastric adenocarcinoma identifies recurrent somatic mutations in cell adhesion and chromatin remodeling genes
Zang, Zhi Jiang et al., 2012 NATURE GENETICS [Article]

Exome sequencing identifies MVK mutations in disseminated superficial actinic porokeratosis
Zhang, Sheng-Quan et al., 2012 NATURE GENETICS [Article]

Exome sequencing identifies truncating mutations in PRRT2 that cause paroxysmal kinesigenic dyskinesia
Chen, Wan-Jin et al., 2011 NATURE GENETICS [Article]

Bayesian inference of ancient human demography from individual genome sequences
Gronau, Ilan et al., 2011 NATURE GENETICS [Article]

Frequent mutations of chromatin remodeling genes in transitional cell carcinoma of the bladder
Gui, Yaoting et al., 2011 NATURE GENETICS [Article]

A rare penetrant mutation in CFH confers high risk of age-related macular degeneration
Raychaudhuri, Soumya et al., 2011 NATURE GENETICS [Article]

Comparing strategies to fine-map the association of common SNPs at chromosome 9p21 with type 2 diabetes and myocardial infarction
Shea, Jessica et al., 2011 NATURE GENETICS [Article]

Inactivating Variants in ANGPTL4 and Risk of Coronary Artery Disease
Dewey, Frederick F. et al., 2016 NEW ENGLAND JOURNAL OF MEDICINE [Article] [Pubmed]

TREM2 Variants in Alzheimer's Disease
Guerreiro, Rita et al., 2013 NEW ENGLAND JOURNAL OF MEDICINE [Article]

SF3B1 and Other Novel Cancer Genes in Chronic Lymphocytic Leukemia
Wang, Lili et al., 2011 NEW ENGLAND JOURNAL OF MEDICINE [Article]

A Systematic Survey of Loss-of-Function Variants in Human Protein-Coding Genes
MacArthur, Daniel G et al., 2012 SCIENCE [Article]

A High-Coverage Genome Sequence from an Archaic Denisovan Individual
Meyer, Matthias et al., 2012 SCIENCE [Article]

Comment on ``Widespread RNA and DNA Sequence Differences in the Human Transcriptome''
Pickrell, Joseph K et al., 2012 SCIENCE [Article]

Browse the citations list separately for each GATK paper. GATK papers that have not yet been cited, are not indexed in Pubmed or have no feed available in WebOfScience are not shown.


The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data
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Frequent somatic CDH1 loss-of-function mutations in plasmacytoid variant bladder cancer
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Chimeric EWSR1-FLI1 regulates the Ewing sarcoma susceptibility gene EGR2 via a GGAA microsatellite
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Genetic evidence for two founding populations of the Americas
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Parent-progeny sequencing indicates higher mutation rates in heterozygotes
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Sparse whole-genome sequencing identifies two loci for major depressive disorder
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Germline mutation rates and the long-term phenotypic effects of mutation accumulation in wild-type laboratory mice and mutator mice
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Relapsed neuroblastomas show frequent RAS-MAPK pathway mutations
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Rare A2ML1 variants confer susceptibility to otitis media
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Loss-of-function variants in ATM confer risk of gastric cancer
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Massively parallel quantification of the regulatory effects of noncoding genetic variation in a human cohort
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Whole-genome characterization of chemoresistant ovarian cancer
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Comprehensive models of human primary and metastatic colorectal tumors in immunodeficient and immunocompetent mice by chemokine targeting
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Loss of delta-catenin function in severe autism
Turner, Tychele N. et al., 2015 NATURE [Article] [Pubmed]

Large-scale whole-genome sequencing of the Icelandic population
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Germline mutations in ETV6 are associated with thrombocytopenia, red cell macrocytosis and predisposition to lymphoblastic leukemia
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Polyploidy can drive rapid adaptation in yeast
Selmecki, Anna M. et al., 2015 NATURE [Article] [Pubmed]

Stromal gene expression defines poor-prognosis subtypes in colorectal cancer
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Whole-genome and multisector exome sequencing of primary and post-treatment glioblastoma reveals patterns of tumor evolution
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Resequencing 302 wild and cultivated accessions identifies genes related to domestication and improvement in soybean
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Combined hereditary and somatic mutations of replication error repair genes result in rapid onset of ultra-hypermutated cancers
Shlien, Adam et al., 2015 NATURE GENETICS [Article] [Pubmed]

Adaptation and possible ancient interspecies introgression in pigs identified by whole-genome sequencing
Ai, Huashui et al., 2015 NATURE GENETICS [Article] [Pubmed]

Genetic and phenotypic intra-species variation in Candida albicans
Hirakawa, Matthew P. et al., 2015 GENOME RESEARCH [Article] [Pubmed]

A recurrent de novo mutation in KCNC1 causes progressive myoclonus epilepsy
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A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping
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The contribution of de novo coding mutations to autism spectrum disorder
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Rapid modelling of cooperating genetic events in cancer through somatic genome editing
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Estimating genotype error rates from high-coverage next-generation sequence data
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Large-scale identification of chemically induced mutations in Drosophila melanogaster
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Ancient human genomes suggest three ancestral populations for present-day Europeans
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Multi-platform assessment of transcriptome profiling using RNA-seq in the ABRF next-generation sequencing study
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Clonal evolution in breast cancer revealed by single nucleus genome sequencing
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A common Greenlandic TBC1D4 variant confers muscle insulin resistance and type 2 diabetes
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Integrating mapping-, assembly- and haplotype-based approaches for calling variants in clinical sequencing applications
Rimmer, Andy et al., 2014 NATURE GENETICS [Article] [Pubmed]

Whole-genome sequence variation, population structure and demographic history of the Dutch population
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Somatic mutations found in the healthy blood compartment of a 115-yr-old woman demonstrate oligoclonal hematopoiesis
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Identification of genomic alterations in oesophageal squamous cell cancer
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Mutations in TJP2 cause progressive cholestatic liver disease
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doublesex is a mimicry supergene
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A recurrent inactivating mutation in RHOA GTPase in angioimmunoblastic T cell lymphoma
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A cascade of DNA-binding proteins for sexual commitment and development in Plasmodium
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Integrating human sequence data sets provides a resource of benchmark SNP and indel genotype calls
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Derived immune and ancestral pigmentation alleles in a 7,000-year-old Mesolithic European
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Exome sequencing identifies BRAF mutations in papillary craniopharyngiomas
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Landscape of genomic alterations in cervical carcinomas
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Simultaneous identification and prioritization of variants in familial, de novo, and somatic genetic disorders with VariantMaster
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A novel method for detecting uniparental disomy from trio genotypes identifies a significant excess in children with developmental disorders
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Loss-of-function mutations in MICU1 cause a brain and muscle disorder linked to primary alterations in mitochondrial calcium signaling
Logan, Clare V. et al., 2014 NATURE GENETICS [Article] [Pubmed]

Variation in chromatin accessibility in human kidney cancer links H3K36 methyltransferase loss with widespread RNA processing defects
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Whole-genome haplotype reconstruction using proximity-ligation and shotgun sequencing
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Whole-genome and whole-exome sequencing of bladder cancer identifies frequent alterations in genes involved in sister chromatid cohesion and segregation
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The haplotype-resolved genome and epigenome of the aneuploid HeLa cancer cell line
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Genome Sequencing Reveals Loci under Artificial Selection that Underlie Disease Phenotypes in the Laboratory Rat
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Genotype calling and haplotyping in parent-offspring trios
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Mutations in GNAL cause primary torsion dystonia
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TREM2 Variants in Alzheimer's Disease
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Read and assembly metrics inconsequential for clinical utility of whole-genome sequencing in mapping outbreaks
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A rare nonsynonymous sequence variant in C3 is associated with high risk of age-related macular degeneration
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Single molecule molecular inversion probes for targeted, high-accuracy detection of low-frequency variation
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The mutational landscape of adenoid cystic carcinoma
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Rare allelic forms of PRDM9 associated with childhood leukemogenesis
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The Next-Generation Sequencing Revolution and Its Impact on Genomics
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SOAPindel: Efficient identification of indels from short paired reads
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DREAMing of a patent-free human genome for clinical sequencing
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Relapse-specific mutations in NT5C2 in childhood acute lymphoblastic leukemia
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Cell-type, allelic, and genetic signatures in the human pancreatic beta cell transcriptome
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Mutations in TUBG1, DYNC1H1, KIF5C and KIF2A cause malformations of cortical development and microcephaly
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Desmoglein 1 deficiency results in severe dermatitis, multiple allergies and metabolic wasting
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Rare variants in CFI, C3 and C9 are associated with high risk of advanced age-related macular degeneration
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A recurrent germline PAX5 mutation confers susceptibility to pre-B cell acute lymphoblastic leukemia
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Genomic architecture of adaptive color pattern divergence and convergence in Heliconius butterflies
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An integrative variant analysis pipeline for accurate genotype/haplotype inference in population NGS data
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An in-frame deletion at the polymerase active site of POLD1 causes a multisystem disorder with lipodystrophy
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The draft genome of sweet orange (Citrus sinensis)
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Genetic programs in human and mouse early embryos revealed by single-cell RNA sequencing
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Comprehensive genome- and transcriptome-wide analyses of mutations associated with microsatellite instability in Korean gastric cancers
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A heterozygous moth genome provides insights into herbivory and detoxification
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Identification of a rare coding variant in complement 3 associated with age-related macular degeneration
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Estimating the human mutation rate using autozygosity in a founder population
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Analysis of the Saccharomyces cerevisiae pan-genome reveals a pool of copy number variants distributed in diverse yeast strains from differing industrial environments
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Genomic Landscape of Non-Small Cell Lung Cancer in Smokers and Never-Smokers
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Recurrent mutations in the U2AF1 splicing factor in myelodysplastic syndromes
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Integrative analysis of genome-wide loss of heterozygosity and monoallelic expression at nucleotide resolution reveals disrupted pathways in triple-negative breast cancer
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Exome sequencing of hepatitis B virus-associated hepatocellular carcinoma
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De novo assembly and genotyping of variants using colored de Bruijn graphs
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Genome-wide genetic changes during modern breeding of maize
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Exome sequencing and the genetic basis of complex traits
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Mutations in NMNAT1 cause Leber congenital amaurosis and identify a new disease pathway for retinal degeneration
Koenekoop, Robert K et al., 2012 NATURE GENETICS [Article]

Rate of de novo mutations and the importance of father's age to disease risk
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Impaired intrinsic immunity to HSV-1 in human iPSC-derived TLR3-deficient CNS cells
Lafaille, Fabien G et al., 2012 NATURE [Article]

Detecting and annotating genetic variations using the HugeSeq pipeline
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Performance comparison of whole-genome sequencing platforms
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Mutations at a single codon in Mad homology 2 domain of SMAD4 cause Myhre syndrome
Le Goff, Carine et al., 2012 NATURE GENETICS [Article]

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Mutations in UVSSA cause UV-sensitive syndrome and impair RNA polymerase IIo processing in transcription-coupled nucleotide-excision repair
Nakazawa, Yuka et al., 2012 NATURE GENETICS [Article]

The malaria parasite Plasmodium vivax exhibits greater genetic diversity than Plasmodium falciparum
Neafsey, Daniel E et al., 2012 NATURE GENETICS [Article]

Patterns and rates of exonic de novo mutations in autism spectrum disorders
Neale, Benjamin M et al., 2012 NATURE [Article]

Extremely low-coverage sequencing and imputation increases power for genome-wide association studies
Pasaniuc, Bogdan et al., 2012 NATURE GENETICS [Article]

Optimized filtering reduces the error rate in detecting genomic variants by short-read sequencing
Reumers, Joke et al., 2012 NATURE BIOTECHNOLOGY [Article]

De novo mutations in the actin genes ACTB and ACTG1 cause Baraitser-Winter syndrome
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Mutations in SWI/SNF chromatin remodeling complex gene ARID1B cause Coffin-Siris syndrome
Santen, Gijs W E et al., 2012 NATURE GENETICS [Article]

Joint genotyping on the fly: Identifying variation among a sequenced panel of inbred lines
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Whole genome sequencing of matched primary and metastatic acral melanomas
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Heterozygous missense mutations in SMARCA2 cause Nicolaides-Baraitser syndrome
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Mutations in the RNA exosome component gene EXOSC3 cause pontocerebellar hypoplasia and spinal motor neuron degeneration
Wan, Jijun et al., 2012 NATURE GENETICS [Article]

Interpreting noncoding genetic variation in complex traits and human disease
Ward, Lucas D et al., 2012 NATURE BIOTECHNOLOGY [Article]

ISPD loss-of-function mutations disrupt dystroglycan O-mannosylation and cause Walker-Warburg syndrome
Willer, Tobias et al., 2012 NATURE GENETICS [Article]

Exome sequencing of gastric adenocarcinoma identifies recurrent somatic mutations in cell adhesion and chromatin remodeling genes
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Exome sequencing identifies MVK mutations in disseminated superficial actinic porokeratosis
Zhang, Sheng-Quan et al., 2012 NATURE GENETICS [Article]

Seventy-five genetic loci influencing the human red blood cell
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Exome sequencing identifies truncating mutations in PRRT2 that cause paroxysmal kinesigenic dyskinesia
Chen, Wan-Jin et al., 2011 NATURE GENETICS [Article]

Performance comparison of exome DNA sequencing technologies
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Bayesian inference of ancient human demography from individual genome sequences
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Frequent mutations of chromatin remodeling genes in transitional cell carcinoma of the bladder
Gui, Yaoting et al., 2011 NATURE GENETICS [Article]

Haplotype-resolved genome sequencing of a Gujarati Indian individual
Kitzman, Jacob O et al., 2011 NATURE BIOTECHNOLOGY [Article]

SNP detection and genotyping from low-coverage sequencing data on multiple diploid samples
Le, Si Quang et al., 2011 GENOME RESEARCH [Article]

Inference of human population history from individual whole-genome sequences
Li, Heng et al., 2011 NATURE [Article]

Low-coverage sequencing: Implications for design of complex trait association studies
Li, Yun et al., 2011 GENOME RESEARCH [Article]

The Human Mitochondrial Transcriptome
Mercer, Tim R et al., 2011 CELL [Article]

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