Daniel Koboldt

107 posts · 108,555 views

Dan Koboldt is works in the medical genomics group of The Genome Center at Washington University.

Massgenomics
107 posts

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  • November 21, 2014
  • 01:58 PM
  • 76 views

Genome, Evolution, and Domestication of the Cat

by Daniel Koboldt in Massgenomics

Even though most of my posts on MassGenomics concern human genetics and genomics, today I’d like to highlight a milestone in another species, one that many humans care fiercely about. This guy: Cat lovers, rejoice! This month in the Proceedings of the National Academy of Sciencs, Mike Montague, Wes Warren, and colleagues published the first complete […]... Read more »

Montague MJ, Li G, Gandolfi B, Khan R, Aken BL, Searle SM, Minx P, Hillier LW, Koboldt DC, Davis BW.... (2014) Comparative analysis of the domestic cat genome reveals genetic signatures underlying feline biology and domestication. Proceedings of the National Academy of Sciences of the United States of America. PMID: 25385592  

  • September 24, 2014
  • 11:42 AM
  • 195 views

Genetics "Experts" Surveyed on Returning Incidental Findings

by Daniel Koboldt in Massgenomics

In my last post, I wrote about the return of results from next-gen sequencing, specifically a recent paper in AJHG about secondary findings in ~6500 ESP exomes. Today we’ll delve into another paper in the same issue on the attitudes of genetics professionals on return of incidental findings from whole genome sequencing (WGS) and exome sequencing […]... Read more »

  • September 10, 2014
  • 08:00 AM
  • 190 views

Return of Results from Next-gen Sequencing

by Daniel Koboldt in Massgenomics

The rapid adoption of next-gen exome and genome sequencing for clinical use (i.e. with patient DNA) raises some difficult questions about the return of results to patients and their families. In contrast to traditional genetic testing, which usually checks for variants in specific genes, high-throughput sequencing has the potential to reveal a number of secondary […]... Read more »

  • May 23, 2014
  • 12:18 PM
  • 91 views

Promoters and Enhancers in the Human Genome

by Daniel Koboldt in Massgenomics

A recent issue of Nature featured two articles from the FANTOM5 project, an effort to systematically study gene expression and regulation by performingg capped analysis of gene expression (CAGE) across a diversity of cell types. FANTOM5 has generated single molecule CAGE profiles for 574 primary human cell samples, each sequenced to a median depth of […]... Read more »

FANTOM Consortium and the RIKEN PMI and CLST (DGT). (2014) A promoter-level mammalian expression atlas. Nature, 507(7493), 462-70. PMID: 24670764  

Andersson R, Gebhard C, Miguel-Escalada I, Hoof I, Bornholdt J, Boyd M, Chen Y, Zhao X, Schmidl C, Suzuki T.... (2014) An atlas of active enhancers across human cell types and tissues. Nature, 507(7493), 455-61. PMID: 24670763  

  • May 6, 2014
  • 11:12 AM
  • 322 views

Prioritizing Variants with Gene and Phenotype Knowledge

by Daniel Koboldt in Massgenomics

Exome and whole-genome sequencing offer powerful assays for disease diagnosis in clinical settings. In theory, they can help uncover the de novo mutations or inherited alleles responsible for rare genetic diseases. Over the past few years, several groups have developed strategies for filtering or prioritizing variants based on their likelihood to cause disease. Our tool, […]... Read more »

  • April 11, 2014
  • 12:46 PM
  • 395 views

Variant Annotation in Coding Regions

by Daniel Koboldt in Massgenomics

The analysis of NGS data comes with many challenges — data management, read alignment, variant calling, etc. — that the bioinformatics community has tackled with some success. Today I want to discuss another critical component of analysis that remains an unsolved problem: annotation of genetic variants. This process, in which we try to predict the […]... Read more »

Davis J McCarthy, Peter Humburg, Alexander Kanapin, Manuel A Rivas, Kyle Gaulton, The WGS500 Consortium, Jean-Baptiste Cazier and Peter Donnelly. (2014) Choice of transcripts and software has a large effect on variant annotation. Genome Medicine, 6(26). info:/doi:10.1186/gm543

  • March 11, 2014
  • 11:33 AM
  • 277 views

Variant Prioritization in Rare Mendelian Disorders

by Daniel Koboldt in Massgenomics

Few areas of biomedical research have benefited more from next-gen sequencing than studies of rare inherited diseases. Rapid, inexpensive exome sequencing in individuals with rare, presumably-monogenic diseases has been hugely successful over the past few years. There’s been a lot of discussion in the NGS community about the analysis burden of the large-scale whole-genome sequencing […]... Read more »

Koboldt DC, Larson DE, Sullivan LS, Bowne SJ, Steinberg KM, Churchill JD, Buhr AC, Nutter N, Pierce EA, Blanton SH.... (2014) Exome-Based Mapping and Variant Prioritization for Inherited Mendelian Disorders. American journal of human genetics. PMID: 24560519  

  • December 19, 2013
  • 10:47 AM
  • 647 views

Evolution and Transcription Factor Binding of Human Exons

by Daniel Koboldt in Massgenomics

A recent paper in Science has been hyped as the revelation of a new code affecting codon choice and protein evolution. In their study, Andrew Stergachis et al from the University of Washington applied DNAaseI-seq to map transcription factor occupancy across the human exome in 81 different cell types. They found that around 15% of […]... Read more »

Stergachis AB, Haugen E, Shafer A, Fu W, Vernot B, Reynolds A, Raubitschek A, Ziegler S, LeProust EM, Akey JM.... (2013) Exonic transcription factor binding directs codon choice and affects protein evolution. Science (New York, N.Y.), 342(6164), 1367-72. PMID: 24337295  

  • October 11, 2013
  • 12:58 PM
  • 352 views

Functional Variation Uncovered by Transcriptome Sequencing

by Daniel Koboldt in Massgenomics

It is increasingly clear that the annotation and interpretation of sequence variants represents one of the most important challenges in human genetics. With next-gen sequencing, our ability to identify variants — in disease pedigrees, case-control cohorts, and apparently healthy individuals — has rapidly outpaced our ability to say anything about what those variants do. This […]... Read more »

Lappalainen T, Sammeth M, Friedländer MR, 't Hoen PA, Monlong J, Rivas MA, Gonzàlez-Porta M, Kurbatova N, Griebel T, Ferreira PG.... (2013) Transcriptome and genome sequencing uncovers functional variation in humans. Nature, 501(7468), 506-11. PMID: 24037378  

  • September 17, 2013
  • 12:23 PM
  • 363 views

The role of alternative complement pathway in AMD

by Daniel Koboldt in Massgenomics

Three letters to Nature Genetics published (online) this week report the association of a rare nonsynonymous variant in the C3 gene with risk for age-related macular degeneration (AMD). These studies all came from different groups, working primarily with different case-control cohorts. What’s fascinating is how they all arrived at the same answer, at around the same time, but in very different ways. They also shared a starting point, of sorts: the relatively recent association of variants in ........ Read more »

Helgason H, Sulem P, Duvvari MR, Luo H, Thorleifsson G, Stefansson H, Jonsdottir I, Masson G, Gudbjartsson DF, Walters GB.... (2013) A rare nonsynonymous sequence variant in C3 is associated with high risk of age-related macular degeneration. Nature genetics. PMID: 24036950  

Zhan X, Larson DE, Wang C, Koboldt DC, Sergeev YV, Fulton RS, Fulton LL, Fronick CC, Branham KE, Bragg-Gresham J.... (2013) Identification of a rare coding variant in complement 3 associated with age-related macular degeneration. Nature genetics. PMID: 24036949  

Seddon JM, Yu Y, Miller EC, Reynolds R, Tan PL, Gowrisankar S, Goldstein JI, Triebwasser M, Anderson HE, Zerbib J.... (2013) Rare variants in CFI, C3 and C9 are associated with high risk of advanced age-related macular degeneration. Nature genetics. PMID: 24036952  

  • July 26, 2013
  • 10:30 AM
  • 545 views

Genetics of Blindness: Inherited Retinal Diseases

by Daniel Koboldt in Massgenomics

The genetics of inherited vision disorders — notably retinitis pigmentosa (RP) and age-related macular degeneration (AMD) — are an area of intense research. Numerous genes responsible for inherited retinopathies have been identified in the past ten years. At the time of writing, there are at least 242 different genetic disorders, with 202 different genes identified [...]... Read more »

  • April 8, 2013
  • 09:32 AM
  • 389 views

Genotype Imputation Aids eQTL Discovery

by Daniel Koboldt in Massgenomics

There are only about 20,000 genes in the human genome, but they generate a surprising amount of diversity. Given that 0.1% of DNA sequence differs when any two individuals are compared, and only 4% differs when a human and a chimpanzee are compared, it’s clear that protein-coding differences alone can’t account for how we differ [...]... Read more »

  • March 26, 2013
  • 08:31 AM
  • 372 views

Searching for Functional Noncoding Variation

by Daniel Koboldt in Massgenomics

Exome sequencing, which targets the exons of known protein-coding genes in the human genome, is being widely employed by the research community to determine the genetic basis of inherited disease. It’s rapidly becoming the frontline research tool in GWAS follow-ups, tumor-normal comparisons, and studies of Mendelian disorders. The authors of some publications have mistakenly referred [...]... Read more »

  • March 8, 2013
  • 03:58 PM
  • 394 views

Breast Cancer Susceptibility: The Role of Rare Variants

by Daniel Koboldt in Massgenomics

About 1 in 8 women in the U.S. will develop breast cancer at some point in her lifetime. In 2013, an estimated 40,000 breast cancer deaths will occur in the U.S. and 300,000 women will be diagnosed with invasive or in situ malignancies. It’s not only one of the most common cancers, but it’s also [...]... Read more »

  • January 28, 2013
  • 09:09 AM
  • 785 views

Identifying Samples from Genomic Data

by Daniel Koboldt in Massgenomics

In last week's issue of Science, Melissa Gymrek and colleagues from the lab of Yaniv Erlich (Whitehead) report a method for the triangulation the identity of a sample donor using genomic data and public databases.

As a proof-of-principle, they uncovered the identities of about 50 sample donors from the CEPH Utah collection, perhaps the best-studied collection of "anonymous" samples to date. Their approach exploits several facts of this "information age" we live in.... Read more »

Gymrek M, McGuire AL, Golan D, Halperin E, & Erlich Y. (2013) Identifying personal genomes by surname inference. Science (New York, N.Y.), 339(6117), 321-4. PMID: 23329047  

  • January 8, 2013
  • 09:28 AM
  • 835 views

High-impact Journals for Genetics and Genomics

by Daniel Koboldt in Massgenomics

One of the burdens of the information age is that there’s far more content produced than could ever be read by the population. This is categorically true of blogging, but also a fact of research publication. With hundreds of academic journals (ISI indexes over 11,000 science and social science journals) and thousands of articles published [...]... Read more »

  • December 31, 2012
  • 09:33 AM
  • 639 views

Ethical Challenges for Clinical Genome Sequencing

by Daniel Koboldt in Massgenomics

Clinical genome sequencing holds great promise for the diagnosis and treatment of human disease, but also brings many ethical challenges. What if key variants are found in the genome of a patient who died? Should those results be returned to the family, and if so, how? [...]... Read more »

  • December 7, 2012
  • 11:13 AM
  • 798 views

Genomic variation landscape of the gut microbiome

by Daniel Koboldt in Massgenomics

It might surprise you to learn that the majority of genes found in human beings are not our own — they belong to the hundreds of species of bacteria that make up the gut microbiome. Just as the number of human genomes sequenced on next-gen instruments has grown exponentially in recent years, so too have [...]... Read more »

Schloissnig, S., Arumugam, M., Sunagawa, S., Mitreva, M., Tap, J., Zhu, A., Waller, A., Mende, D., Kultima, J., Martin, J.... (2012) Genomic variation landscape of the human gut microbiome. Nature. DOI: 10.1038/nature11711  

  • November 2, 2012
  • 05:56 PM
  • 572 views

Human genetic variation mapped in 1,000 genomes

by Daniel Koboldt in Massgenomics

This week marked an important milestone in our understanding of human genetic variation: the main publication of the 1,000 Genomes Project. The article in Nature describes the genomes from 1,092 individuals representing 14 populations across Europe, Africa, Asia, and the Americas. I think it’s important for anyone working in human genetics and genomics to read [...]... Read more »

  • October 9, 2012
  • 05:00 PM
  • 1,100 views

Redefining the Gene: Transcription Landscape of Human Cells

by Daniel Koboldt in Massgenomics

Using genetic information to improve human health represents the central goal of biomedical research. Achieving it won’t be easy, but from a simplistic perspective, requires three steps. Cataloging the full extent of genetic variation in cells, tissues, and individuals. Efforts like the HapMap and 1,000 Genomes project are tackling this part, and judging by the [...]... Read more »

Djebali S, Davis CA, Merkel A, Dobin A, Lassmann T, Mortazavi A, Tanzer A, Lagarde J, Lin W, Schlesinger F.... (2012) Landscape of transcription in human cells. Nature, 489(7414), 101-8. PMID: 22955620  

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