40 posts · 45,289 views
Genetic Future describes the latest scientific discoveries about human genetic variation, and explains what they mean for your health, your family, and society.
dgmacarthur
40 posts
Sort by: Latest Post, Most Popular
View by: Condensed, Full
- April 29, 2010
- 12:30 PM
- 585 views
Guest post: Kai Wang on the McClellan and King critique of genome-wide association studies
by dgmacarthur in Genetic Future
Kai Wang is a postdoctoral fellow at the Center for Applied Genomics, Children's Hospital of Philadelphia and an author on numerous genome-wide association studies. He left this lengthy comment as a response to my recent post on this comment by McClellan and King in Cell, and I felt it warranted promotion to a full post (with Kai's permission). For more discussion of the M&K review see also two recent posts by Steve Turner at Getting Genetics Done, and an excellent post from p-ter ........ Read more »
McClellan, J., & King, M. (2010) Genetic Heterogeneity in Human Disease. Cell, 141(2), 210-217. DOI: 10.1016/j.cell.2010.03.032
- March 31, 2010
- 10:00 PM
- 782 views
Common copy number variation doesn't explain much complex disease risk - but why not?
by dgmacarthur in Genetic Future
... Read more »
Craddock, N., Hurles, M., Cardin, N., Pearson, R., Plagnol, V., Robson, S., Vukcevic, D., Barnes, C., Conrad, D., Giannoulatou, E.... (2010) Genome-wide association study of CNVs in 16,000 cases of eight common diseases and 3,000 shared controls. Nature, 464(7289), 713-720. DOI: 10.1038/nature08979
- March 10, 2010
- 05:00 PM
- 702 views
Disease hunting with whole genome sequences: the good news, and the bad news
by dgmacarthur in Genetic Future
Lupski, J.R., et al. (2010). Whole-genome sequencing in a patient with Charcot-Marie-Tooth neuropathy. New England Journal of Medicine advance online 10.1056/nejmoa0908094Roach, J.C., & et al. (2010). Analysis of genetic inheritance in a family quartet by whole-genome sequencing. Science : 10.1126/science.1186802[Note that links to the papers may not yet be active.]Two new papers out today - the first ever studies to employ whole-genome sequencing for disease gene discovery - ........ Read more »
Lupski, J.R. (2010) Whole-genome sequencing in a patient with Charcot-Marie-Tooth neuropathy. New England Journal of Medicine. info:/10.1056/nejmoa0908094
Roach, J.C., & et al. (2010) Analysis of genetic inheritance in a family quartet by whole-genome sequencing. Science. info:/10.1126/science.1186802
- November 11, 2009
- 07:15 PM
- 982 views
23andMe gets scooped on hair curl genes
by dgmacarthur in Genetic Future
Medland et al. (2009). Common Variants in the Trichohyalin Gene Are Associated with Straight Hair in Europeans. The American Journal of Human Genetics DOI: 10.1016/j.ajhg.2009.10.009A couple of weeks ago I reported on a presentation by 23andMe's Nick Eriksson at the American Society of Human Genetics meeting in Honolulu, in which Eriksson presented data on a series of genome-wide association studies performed by the company using genetic and trait data from its customers.Along with genetic ........ Read more »
Medland, S., Nyholt, D., Painter, J., McEvoy, B., McRae, A., Zhu, G., Gordon, S., Ferreira, M., Wright, M., & Henders, A. (2009) Common Variants in the Trichohyalin Gene Are Associated with Straight Hair in Europeans. The American Journal of Human Genetics. DOI: 10.1016/j.ajhg.2009.10.009
- August 14, 2009
- 10:45 AM
- 825 views
Making sense of changing risk predictions from personal genomics
by dgmacarthur in Genetic Future
Mihaescu, R., van Hoek, M., Sijbrands, E., Uitterlinden, A., Witteman, J., Hofman, A., van Duijn, C., & Janssens, A. (2009). Evaluation of risk prediction updates from commercial genome-wide scans Genetics in Medicine, 11 (8), 588-594 DOI: 10.1097/GIM.0b013e3181b13a4fCaroline Wright from the Public Health Genomics Foundation has a concise post describing the results from a recent paper in Genetic Medicine. The paper evaluates the probability that personal genomics customers will find that th........ Read more »
Mihaescu, R., van Hoek, M., Sijbrands, E., Uitterlinden, A., Witteman, J., Hofman, A., van Duijn, C., & Janssens, A. (2009) Evaluation of risk prediction updates from commercial genome-wide scans. Genetics in Medicine, 11(8), 588-594. DOI: 10.1097/GIM.0b013e3181b13a4f
- August 10, 2009
- 08:00 PM
- 1,066 views
First human genome sequenced using single-molecule sequencing
by dgmacarthur in Genetic Future
Pushkarev, D., Neff, N., & Quake, S. (2009). Single-molecule sequencing of an individual human genome Nature Biotechnology DOI: 10.1038/nbt.1561Yes, it's yet another "complete" individual genome sequence, following on the heels of Craig Venter, James Watson, an anonymous African male (twice, and not without controversy), a female cancer patient, a Chinese man, and two Koreans. There is a new twist, though: this is the first genome to be sequenced using single molecule sequencing te........ Read more »
Pushkarev, D., Neff, N., & Quake, S. (2009) Single-molecule sequencing of an individual human genome. Nature Biotechnology. DOI: 10.1038/nbt.1561
- August 4, 2009
- 09:45 AM
- 1,071 views
Guest post: Luke Jostins on the twice-sequenced genome
by dgmacarthur in Genetic Future
While I continue my work-induced blog coma, here's a guest post from Luke Jostins, a genetic epidemiology PhD student and the author of the blog Genetic Inference, delivering a fairly scathing critique of a recent whole-genome sequencing paper based on Life Technologies' SOLiD platform.McKernan et al. 2009. Sequence and structural variation in a human genome uncovered by short-read, massively parallel ligation sequencing using two-base encoding Genome Research DOI: 10.1101/gr.091868.109In prepub........ Read more »
McKernan, K., Peckham, H., Costa, G., McLaughlin, S., Fu, Y., Tsung, E., Clouser, C., Duncan, C., Ichikawa, J., Lee, C.... (2009) Sequence and structural variation in a human genome uncovered by short-read, massively parallel ligation sequencing using two-base encoding. Genome Research. DOI: 10.1101/gr.091868.109
- July 17, 2009
- 09:00 AM
- 1,098 views
Guest post: Neil Walker on the curious case of the schizophrenia GWAS
by dgmacarthur in Genetic Future
Purcell et al. (2009). Common polygenic variation contributes to risk of schizophrenia and bipolar disorder Nature DOI: 10.1038/nature08185Neil Walker has been doing a spectacular job of serving up useful information in the comments recently, so I asked him to write the first ever guest post on Genetic Future - something that (as I will be announcing shortly) I intend to do fairly regularly over the next couple of months.The topic is a paper that has created a rather perplexed buzz recently in t........ Read more »
Purcell, S., Wray, N., Stone, J., Visscher, P., O'Donovan, M., Sullivan, P., Sklar, P., Purcell (Leader), S., Stone, J., Sullivan, P.... (2009) Common polygenic variation contributes to risk of schizophrenia and bipolar disorder. Nature. DOI: 10.1038/nature08185
- April 28, 2009
- 12:00 PM
- 1,286 views
Genetics of complex traits in Europeans and East Asians: similarities and differences
by dgmacarthur in Genetic Future
Cho, Y., Go, M., Kim, Y., Heo, J., Oh, J., Ban, H., Yoon, D., Lee, M., Kim, D., Park, M., Cha, S., Kim, J., Han, B., Min, H., Ahn, Y., Park, M., Han, H., Jang, H., Cho, E., Lee, J., Cho, N., Shin, C., Park, T., Park, J., Lee, J., Cardon, L., Clarke, G., McCarthy, M., Lee, J., Lee, J., Oh, B., & Kim, H. (2009). A large-scale genome-wide association study of Asian populations uncovers genetic factors influencing eight quantitative traits Nature Genetics, 41 (5), 527-534 DOI: 10.1038/ng.357A pa........ Read more »
Cho, Y., Go, M., Kim, Y., Heo, J., Oh, J., Ban, H., Yoon, D., Lee, M., Kim, D., Park, M.... (2009) A large-scale genome-wide association study of Asian populations uncovers genetic factors influencing eight quantitative traits. Nature Genetics, 41(5), 527-534. DOI: 10.1038/ng.357
- March 24, 2009
- 06:10 PM
- 1,338 views
Genetic signatures of recent human evolution, continued
by dgmacarthur in Genetic Future
Pickrell, J., Coop, G., Novembre, J., Kudaravalli, S., Li, J., Absher, D., Srinivasan, B., Barsh, G., Myers, R., Feldman, M., & Pritchard, J. (2009). Signals of recent positive selection in a worldwide sample of human populations Genome Research DOI: 10.1101/gr.087577.108I pointed yesterday to a new paper in Genome Research taking a genome-wide look at the signatures of recent natural selection in a worldwide sample of humans.I promised a more thorough analysis of this paper today, but I see Raz........ Read more »
Pickrell, J., Coop, G., Novembre, J., Kudaravalli, S., Li, J., Absher, D., Srinivasan, B., Barsh, G., Myers, R., Feldman, M.... (2009) Signals of recent positive selection in a worldwide sample of human populations. Genome Research. DOI: 10.1101/gr.087577.108
- March 13, 2009
- 06:55 PM
- 1,366 views
The decline of inbreeding, written in our genes
by dgmacarthur in Genetic Future
Nalls, M., Simon-Sanchez, J., Gibbs, J., Paisan-Ruiz, C., Bras, J., Tanaka, T., Matarin, M., Scholz, S., Weitz, C., Harris, T., Ferrucci, L., Hardy, J., & Singleton, A. (2009). Measures of Autozygosity in Decline: Globalization, Urbanization, and Its Implications for Medical Genetics PLoS Genetics, 5 (3) DOI: 10.1371/journal.pgen.1000415A new study indicates that increases in mobility, urbanisation, and cross-population mating over the last century have substantially reduced inbreeding, and ........ Read more »
Nalls, M., Simon-Sanchez, J., Gibbs, J., Paisan-Ruiz, C., Bras, J., Tanaka, T., Matarin, M., Scholz, S., Weitz, C., Harris, T.... (2009) Measures of Autozygosity in Decline: Globalization, Urbanization, and Its Implications for Medical Genetics. PLoS Genetics, 5(3). DOI: 10.1371/journal.pgen.1000415
- March 10, 2009
- 02:15 PM
- 1,366 views
Predicting eye colour from genes
by dgmacarthur in Genetic Future
Fan Liu, Kate van Duijn, Johannes R. Vingerling, Albert Hofman, André G. Uitterlinden, A. Cecile J.W. Janssens, Manfred Kayser (2009). Eye color and the prediction of complex phenotypes from genotypes Current Biology, 19 (5) DOI: 10.1016/j.cub.2009.01.027In a recent post I noted that genetic tests to predict adult height are still a long way off being accurate; currently, known genetic variants can predict just over 5% of the variance in height, as opposed to 40% predicted using a simple algori........ Read more »
Fan Liu, Kate van Duijn, Johannes R. Vingerling, Albert Hofman, André G. Uitterlinden, A. Cecile J.W. Janssens, & Manfred Kayser. (2009) Eye color and the prediction of complex phenotypes from genotypes. Current Biology, 19(5). DOI: 10.1016/j.cub.2009.01.027
- March 6, 2009
- 06:30 AM
- 1,291 views
Rare genetic variants protect against type 1 diabetes
by dgmacarthur in Genetic Future
Nejentsev et al. (2009). Rare Variants of IFIH1, a Gene Implicated in Antiviral Responses, Protect Against Type 1 Diabetes. Science DOI: 10.1126/science.1167728The first item on my long list of predictions for 2009 was that this will be the year of rare variants for common disease - the year that we really start tracking down the low-frequency genetic variants (between 0.1 and 5% in frequency) that likely contribute substantially to the risk of common diseases like arthritis and diabetes. It's f........ Read more »
Nejentsev et al. (2009) Rare Variants of IFIH1, a Gene Implicated in Antiviral Responses, Protect Against Type 1 Diabetes. Science. DOI: 10.1126/science.1167728
- March 5, 2009
- 06:44 PM
- 1,300 views
Finding disease mutations in a sea of noise
by dgmacarthur in Genetic Future
Jones et al. (2009). Exomic Sequencing Identifies PALB2 as a Pancreatic Cancer Susceptibility Gene. Science DOI: 10.1126/science.1171202A paper published online today in Science illustrates both the potential and the challenges of using large-scale DNA sequencing to identify rare genetic variants underlying disease risk.Traditionally, geneticists have pinned down such variants using large family studies. By using these families to track which parts of the genome tend to be co-inherited with the ........ Read more »
Jones et al. (2009) Exomic Sequencing Identifies PALB2 as a Pancreatic Cancer Susceptibility Gene. Science. DOI: 10.1126/science.1171202
- March 3, 2009
- 07:30 AM
- 1,383 views
Predicting height: the Victorian approach beats modern genomics
by dgmacarthur in Genetic Future
Yurii S Aulchenko, Maksim V Struchalin, Nadezhda M Belonogova, Tatiana I Axenovich, Michael N Weedon, Albert Hofman, Andre G Uitterlinden, Manfred Kayser, Ben A Oostra, Cornelia M van Duijn, A Cecile J W Janssens, Pavel M Borodin (2009). Predicting human height by Victorian and genomic methods European Journal of Human Genetics DOI: 10.1038/ejhg.2009.5
Human height is a strongly genetic trait: in well-nourished Westerners somewhere in the vicinity of 80-90% of the variation in height is due to ........ Read more »
Yurii S Aulchenko, Maksim V Struchalin, Nadezhda M Belonogova, Tatiana I Axenovich, Michael N Weedon, Albert Hofman, Andre G Uitterlinden, Manfred Kayser, Ben A Oostra, Cornelia M van Duijn.... (2009) Predicting human height by Victorian and genomic methods. European Journal of Human Genetics. DOI: 10.1038/ejhg.2009.5
- February 23, 2009
- 07:00 AM
- 1,332 views
Direct reading of DNA with protein nanopores: Oxford Nanopore demonstrates proof of principle
by dgmacarthur in Genetic Future
James Clarke, Hai-Chen Wu, Lakmal Jayasinghe, Alpesh Patel, Stuart Reid, Hagan Bayley (2009). Continuous base identification for single-molecule nanopore DNA sequencing Nature Nanotechnology DOI: 10.1038/nnano.2009.12The clever boys and girls at Oxford Nanopore Technologies - one of the most quietly impressive contenders in the hotly-contested next-generation DNA sequencing race - have a new paper out in Nature Nanotechnology today. The paper demonstrates proof of principle for a crucial step in........ Read more »
James Clarke, Hai-Chen Wu, Lakmal Jayasinghe, Alpesh Patel, Stuart Reid, & Hagan Bayley. (2009) Continuous base identification for single-molecule nanopore DNA sequencing. Nature Nanotechnology. DOI: 10.1038/nnano.2009.12
- February 1, 2009
- 12:45 PM
- 1,276 views
The market for designer babies
by dgmacarthur in Genetic Future
Razib points to an article suggesting that Australian couples are "flocking" to a US fertility clinic that allows them to screen their potential IVF embryos for sex and even cosmetic traits like skin and eye colour, in addition to variants that predispose to severe disease risk. ("Flocking", in this context, means about 14 couples a month.)This follows on the heels of a fairly widely-publicised study published last week that surveyed around 1,000 genetic counselling patients about their attitude........ Read more »
Feighanne Hathaway, Esther Burns, & Harry Ostrer. (2009) Consumers’ Desire towards Current and Prospective Reproductive Genetic Testing. Journal of Genetic Counseling. DOI: 10.1007/s10897-008-9199-3
- January 16, 2009
- 10:15 AM
- 1,226 views
Squeezing the genome: how to shrink your whole-genome sequence to 4 MB
by dgmacarthur in Genetic Future
A new paper in Bioinformatics describes an efficient compression algorithm that allows an individual's complete genome sequence to be compressed down to a vanishingly small amount of data - just 4 megabytes (MB).
The paper takes a similar approach to the process I described in a post back in June last year (sheesh, if only I'd thought to write that up as a paper instead!). I estimated using that approach that the genome could be shrunk down to just 20 MB - compared to about 1.5 GB if you stored........ Read more »
S. Christley, Y. Lu, C. Li, & X. Xie. (2008) Human genomes as email attachments. Bioinformatics, 25(2), 274-275. DOI: 10.1093/bioinformatics/btn582
- January 16, 2009
- 06:35 AM
- 1,477 views
The genetic history of Iceland
by dgmacarthur in Genetic Future
Razib has an excellent discussion of a brand new paper in PLoS Genetics, which uses DNA samples from medieval Icelandic skeletons to explore the genetic history of the Icelandic population.
This population is of course of great interest to human geneticists: the Icelandic company deCODE (the home of over half the authors on this paper) has used its exclusive access to the DNA and genealogical and health records of Icelanders to publish vast numbers of studies on the genetic basis of human disea........ Read more »
Agnar Helgason, Carles Lalueza-Fox, Shyamali Ghosh, Sigrún Sigurðardóttir, Maria Lourdes Sampietro, Elena Gigli, Adam Baker, Jaume Bertranpetit, Lilja Árnadóttir, Unnur Þorsteinsdottir.... (2009) Sequences From First Settlers Reveal Rapid Evolution in Icelandic mtDNA Pool. PLoS Genetics, 5(1). DOI: 10.1371/journal.pgen.1000343
- January 9, 2009
- 07:45 AM
- 1,245 views
Genetic differences between human populations: more drift than selection?
by dgmacarthur in Genetic Future
T. Hofer, N. Ray, D. Wegmann, L. Excoffier (2009). Large allele frequency differences between human continental groups are more likely to have occurred by drift during range expansions than by selection Annals of Human Genetics, 73 (1), 95-108 DOI: 10.1111/j.1469-1809.2008.00489.x
I've just been reading over an article from late last year in the Annals of Human Genetics:
In this study, we examined 772 STRs, 210 diallelic indels, and 2834 SNPs typed in 53 human populations worldwide under the H........ Read more »
T. Hofer, N. Ray, D. Wegmann, & L. Excoffier. (2009) Large Allele Frequency Differences between Human Continental Groups are more Likely to have Occurred by Drift During range Expansions than by Selection. Annals of Human Genetics, 73(1), 95-108. DOI: 10.1111/j.1469-1809.2008.00489.x
topics
join us!
Do you write about peer-reviewed research in your blog? Use ResearchBlogging.org to make it easy for your readers — and others from around the world — to find your serious posts about academic research.
If you don't have a blog, you can still use our site to learn about fascinating developments in cutting-edge research from around the world.
