96 posts · 83,294 views
Dan Koboldt blogs about human genetics, genomics, and DNA sequencing in the post-genome era.
Daniel Koboldt
96 posts
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- April 8, 2013
- 09:32 AM
- 88 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 »
Liang L, Morar N, Dixon AL, Lathrop GM, Abecasis GR, Moffatt MF, & Cookson WO. (2013) A cross-platform analysis of 14,177 expression quantitative trait loci derived from lymphoblastoid cell lines. Genome research, 23(4), 716-26. PMID: 23345460
- March 26, 2013
- 08:31 AM
- 53 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 »
Rada-Iglesias A, & Wysocka J. (2011) Epigenomics of human embryonic stem cells and induced pluripotent stem cells: insights into pluripotency and implications for disease. Genome medicine, 3(6), 36. PMID: 21658297
- March 8, 2013
- 03:58 PM
- 44 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 »
Gracia-Aznarez FJ, Fernandez V, Pita G, Peterlongo P, Dominguez O, de la Hoya M, Duran M, Osorio A, Moreno L, Gonzalez-Neira A.... (2013) Whole Exome Sequencing Suggests Much of Non-BRCA1/BRCA2 Familial Breast Cancer Is Due to Moderate and Low Penetrance Susceptibility Alleles. PloS one, 8(2). PMID: 23409019
- January 28, 2013
- 09:09 AM
- 430 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
- 282 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 »
Tort, A., Targino, Z., & Amaral, O. (2012) Rising Publication Delays Inflate Journal Impact Factors. PLoS ONE, 7(12). DOI: 10.1371/journal.pone.0053374
- December 31, 2012
- 09:33 AM
- 303 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 »
Chan, B., Facio, F., Eidem, H., Hull, S., Biesecker, L., & Berkman, B. (2012) Genomic Inheritances: Disclosing Individual Research Results From Whole-Exome Sequencing to Deceased Participants’ Relatives. The American Journal of Bioethics, 12(10), 1-8. DOI: 10.1080/15265161.2012.699138
- December 7, 2012
- 11:13 AM
- 490 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
- 223 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 »
The 1000 Genomes Project Consortium. (2012) An integrated map of genetic variation from 1,092 human genomes. Nature. DOI: 10.1038/nature11632
- October 9, 2012
- 05:00 PM
- 790 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
- September 24, 2012
- 11:38 AM
- 609 views
A comprehensive atlas of breast cancer genomes
by Daniel Koboldt in Massgenomics
Now online at Nature is the most comprehensive molecular portrait of human breast tumors published to date. The Cancer Genome Atlas study encompasses more than 500 primary tumors representing the four intrinsic subtypes of breast cancer: Luminal A, Luminal B, Her2-enriched, and Basal-like. Using a suite of high-throughput platforms, TCGA characterized various aspects of these [...]... Read more »
The Cancer Genome Atlas Network. (2012) Comprehensive Molecular Portraits of Human Breast Tumors. Nature. DOI: 10.1038/nature11412
- September 18, 2012
- 01:56 PM
- 401 views
ENCODE Reveals Regulatory Variation in the Human Genome
by Daniel Koboldt in Massgenomics
I’m still working through the outstanding series of articles published by members of the ENCODE Consortium. After my previous post highlighting their marker paper on genome content and function, I came across two companion papers that demonstrate the power of ENCODE data to characterize functional regulatory variants in the human genome. The first article, from [...]... Read more »
Vernot B, Stergachis AB, Maurano MT, Vierstra J, Neph S, Thurman RE, Stamatoyannopoulos JA, & Akey JM. (2012) Personal and population genomics of human regulatory variation. Genome research, 22(9), 1689-97. PMID: 22955981
Schaub MA, Boyle AP, Kundaje A, Batzoglou S, & Snyder M. (2012) Linking disease associations with regulatory information in the human genome. Genome research, 22(9), 1748-59. PMID: 22955986
- August 17, 2012
- 08:56 AM
- 287 views
Sample Challenges in an Era of Pervasive Sequencing
by Daniel Koboldt in Massgenomics
Next-generation sequencing is a disruptive technology. It’s changed the way we conduct genetic and genomic research, and perhaps more importantly, where that research takes place. Because high-throughput sequencing is accessible not just to large genome centers but to the wider research community. With this “democratization” of sequencing, many things are changing. Virtually any investigator can [...]... Read more »
Yost SE, Smith EN, Schwab RB, Bao L, Jung H, Wang X, Voest E, Pierce JP, Messer K, Parker BA.... (2012) Identification of high-confidence somatic mutations in whole genome sequence of formalin-fixed breast cancer specimens. Nucleic acids research, 40(14). PMID: 22492626
- August 10, 2012
- 10:13 AM
- 403 views
De novo mutations and human disease
by Daniel Koboldt in Massgenomics
Many, if not most human diseases have a genetic component. Thanks to advances in next-gen sequencing, a plethora of studies in recent years have shed light on the role of germline variants in heritable diseases, and of somatic mutations in cancer. They are also beginning to unravel the role of true de novo mutations — [...]... Read more »
Veltman JA, & Brunner HG. (2012) De novo mutations in human genetic disease. Nature reviews. Genetics, 13(8), 565-75. PMID: 22805709
- July 26, 2012
- 09:37 AM
- 326 views
Aging, Mutations, and Leukemia
by Daniel Koboldt in Massgenomics
A study now online at Cell employs has revealed new insights about the normal processes of aging and mutation, and their role in development of acute myeloid leukemia (AML). Cells from the founding clone sometimes acquired additional cooperating mutations (e.g. FLT3), yielding subclones that may have contributed to progression or relapse. These findings reinforce many [...]... Read more »
Welch JS, Ley TJ, Link DC, Miller CA, Larson DE, Koboldt DC, Wartman LD, Lamprecht TL, Liu F, Xia J.... (2012) The origin and evolution of mutations in acute myeloid leukemia. Cell, 150(2), 264-78. PMID: 22817890
- July 17, 2012
- 11:42 AM
- 621 views
Elusive Mendelian Disease Genes: 6 Possible Explanations
by Daniel Koboldt in Massgenomics
Next-gen sequencing has helped elucidate the genetic basis of numerous inherited diseases. Single-gene Mendelian disorders, while rare, are the lowest-hanging fruit for such discoveries. They’re rare, they run in families, and they presumably are caused by a single mutation shared by all affected individuals. Getting the samples is usually the hard part; once that’s done, [...]... Read more »
Li MX, Gui HS, Kwan JS, Bao SY, & Sham PC. (2012) A comprehensive framework for prioritizing variants in exome sequencing studies of Mendelian diseases. Nucleic acids research, 40(7). PMID: 22241780
- July 5, 2012
- 03:21 PM
- 859 views
Finding Mutation Significance in Cancer
by Daniel Koboldt in Massgenomics
Just published in Genome Research: A new tool with a mellifluous name is now available for the analysis of large-scale cancer sequencing data sets. The Mutation Significance In Cancer (MuSiC) package is a suite of tools for identifying significant mutations, relationships, and correlations in a mutation dataset. Contents: Mutation Analysis Tools MuSiC Requirements MuSiC Applications [...]... Read more »
Nathan D. Dees, Qunyuan Zhang, Cyriac Kandoth, Michael C. Wendl, William Schierding, Daniel C. Koboldt, Thomas B. Mooney, Matthew B. Callaway, David Dooling, Elaine R. Mardis Richard K. Wilson and Li Ding. (2012) MuSiC: Identifying mutational significance in cancer genomes. Genome Research. info:/10.1101/gr.134635.111
- June 29, 2012
- 12:12 PM
- 883 views
Breast Cancer Sequencing by Aromatase Inhibitor Response
by Daniel Koboldt in Massgenomics
This month, Matthew J. Ellis and colleagues reported the whole-genome and/or exome sequencing of 77 estrogen-receptor-positive (ER+) breast cancer patients enrolled in a clinical trial of aromatase inhibitors. Their findings provide new insights into the genetic mechanisms of AI resistance, and may help pave the way to personalized cancer treatment in breast cancer. Breast Cancer [...]... Read more »
Ellis MJ, Ding L, Shen D, Luo J, Suman VJ, Wallis JW, Van Tine BA, Hoog J, Goiffon RJ, Goldstein TC.... (2012) Whole-genome analysis informs breast cancer response to aromatase inhibition. Nature, 486(7403), 353-60. PMID: 22722193
- June 13, 2012
- 03:24 PM
- 263 views
On the Interpretation of Human Genomes
by Daniel Koboldt in Massgenomics
Today, if you could find someone to do it, you might have your genome sequenced for around $10,000. You would receive a list of your ~3 million genetic variants: predominantly base substituations (SNPs), but also insertions or deletions (indels) and larger structural changes (e.g. copy number variants). And you would probably have no idea what [...]... Read more »
MacArthur DG, Balasubramanian S, Frankish A, Huang N, Morris J, Walter K, Jostins L, Habegger L, Pickrell JK, Montgomery SB.... (2012) A systematic survey of loss-of-function variants in human protein-coding genes. Science (New York, N.Y.), 335(6070), 823-8. PMID: 22344438
- June 1, 2012
- 11:21 AM
- 440 views
Clinical Exome Sequencing: Hope for Rare Genetic Diseases?
by Daniel Koboldt in Massgenomics
Biomedical researchers have often been insulated from the patients they’re studying. At such a distance, it’s sometimes hard to appreciate the day-to-day struggle of people with genetic diseases. That’s why I like this dual perspective: A clinical study of 12 patients with undiagnosed diseases, and one father's chronicle of his family's struggle to understand their son's disease.... Read more »
Need AC, Shashi V, Hitomi Y, Schoch K, Shianna KV, McDonald MT, Meisler MH, & Goldstein DB. (2012) Clinical application of exome sequencing in undiagnosed genetic conditions. Journal of medical genetics. PMID: 22581936
- May 25, 2012
- 11:54 AM
- 396 views
Integrative Copy Number Analysis of Cancer Exomes
by Daniel Koboldt in Massgenomics
Cancer genomes often harbor numerous types of genetic alterations - mutations, structural variation, gene conversion events, etc. No single approach can survey everything at once, but exome sequencing is advantageous because mutations, copy number changes, and zygosity changes can be characterized simultaneously.... Read more »
Koboldt DC, Zhang Q, Larson DE, Shen D, McLellan MD, Lin L, Miller CA, Mardis ER, Ding L, & Wilson RK. (2012) VarScan 2: Somatic mutation and copy number alteration discovery in cancer by exome sequencing. Genome research. PMID: 22300766
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