Journal Club 4/16/2010

Our Program in Computation Genomics Journal Club is starting again, now the 3rd Friday of each month. The next meeting is this Friday, April 16, at 3pm in the CHGR conference room. As usual, please bring in any articles you've found recently and give a brief overview of why you thought it was interesting. Also, take a look at these papers related to BioVU by investigators at Vanderbilt:

The BioVU demonstration project:

Ritchie MD, Denny JC, Crawford DC, Ramirez AH, Weiner JB, Pulley JM, Basford MA, Brown-Gentry K, Balser JR, Masys DR, Haines JL, Roden DM. Robust Replication of Genotype-Phenotype Associations across Multiple Diseases in an Electronic Medical Record. Am J Hum Genet. 2010 Mar 31.

 
The PheWAS:

Denny JC, Ritchie MD, Basford M, Pulley J, Bastarache L, Brown-Gentry K, Wang D, Masys DR, Roden DM, Crawford DC. PheWAS: Demonstrating the feasibility of a phenome-wide scan to discover gene-disease associations. Bioinformatics. 2010 Mar 24.


And finally, the PNAS paper from Brad Malin's group, which has generated quite a lot of press (Nature News, Technology Review, Genomics Law Report):

Loukides G, Gkoulalas-Divanis A, Malin B. Anonymization of electronic medical records for validating genome-wide association studies. PNAS.

Papers from March 8, 2010 Journal Club

Here are the papers we talked about in yesterday's Journal Club:

Genome Biol. 2009; 10(11): R134
Searching for SNPs with cloud computing.
Langmead B, Schatz MC, Lin J, Pop M, Salzberg SL.

Table of Contents, Nature Methods, Visualization Supplement.

Am J Hum Genet. 2010 Feb 12; 86(2): 113-25
Functional gene group analysis reveals a role of synaptic heterotrimeric G proteins in cognitive ability.
Ruano D, Abecasis GR, Glaser B, Lips ES, Cornelisse LN, de Jong AP, Evans DM, Smith DG, Timpson NJ, SMit AB, Heutink P, Verhage M, Posthuma D.

"Synthetic associations" - an alternative point of view

If you read the previously mentioned "synthetic associations" paper in PLoS Bio by Dickson et al. in David Goldstein's group, be sure to read this brief commentary written by Pat Sullivan at UNC offering a different point of view. The original paper created the liveliest discussion we've had in journal club since we talked about the ISC en masse paper, and Sullivan's commentary very nicely mirrors some of our own thoughts on the paper that were brought up at journal club last week.

Patrick Sullivan: “Synthetic” Ado About Nothing?

Papers from Feb 8 2010 Journal Club

Here are the papers we talked about in yesterday's Journal Club:

PLoS Biol. 2010 Jan 26;8(1):e1000294.
Rare variants create synthetic genome-wide associations. See my previous coverage of this paper and the comments.
Dickson SP, Wang K, Krantz I, Hakonarson H, Goldstein DB.

PLoS Genet. 2010 Jan;6(1):e1000798. Epub 2010 Jan 8.
Modeling of environmental effects in genome-wide association studies identifies SLC2A2 and HP as novel loci influencing serum cholesterol levels.
Igl W, Johansson A, Wilson JF, Wild SH, Polasek O, Hayward C, Vitart V, Hastie N, Rudan P, Gnewuch C, Schmitz G, Meitinger T, Pramstaller PP, Hicks AA, Oostra BA, van Duijn CM, Rudan I, Wright A, Campbell H, Gyllensten U; EUROSPAN Consortium.

Science. 2010 Jan 7. [Epub ahead of print]
A Composite of Multiple Signals Distinguishes Causal Variants in Regions of Positive Selection.
Grossman SR, Shylakhter I, Karlsson EK, Byrne EH, Morales S, Frieden G, Hostetter E, Angelino E, Garber M, Zuk O, Lander ES, Schaffner SF, Sabeti PC.

Computational Genomics Journal Club, Monday Feb 8

We're restarting the PCG Journal Club again Monday February 8 at 4pm in the CHGR conference room. Most of you who usually attend are familiar with the format, but if not, bring any papers you've read recently and give a brief (i.e. 2 minute) overview of the paper and why you thought it was interesting. No slides allowed. We're also going to discuss the previously mentioned Rare Variants Create Synthetic Associations paper recently published in PLoS Biology, which has generated a bit of controversy lately.  Oh yeah, and we'll have beer and snacks.  In case you miss it, Julia will be posting links to all the papers we discuss under the Journal Club tag. You can also view any of the papers from previous journal clubs under that link.

PCG Journal Club Articles, 9/11

There were only a couple of citations for articles discussed at this week's PCG meeting (September 11). Our next meeting is scheduled for September 26.

~Julia

Kim S, Xing EP. Statistical estimation of correlated genome associations to a quantitative trait network. PLoS Genet. 2009 Aug; 5(8):e1000587.

Zamar D, Tripp B, Ellis G, Daley D. Path: a tool to failitate pathway-based genetic association analysis. Bioinformatics. 2009 Sep 15; 25(18):2444-6

PCG Journal Club Articles, 8/28

Here are citations for the articles discussed at our most recent meeting (August 28). I have also appended a link to Nature Reviews: Genetics new series, Fundamental concepts in genetics, at the end. Our next meeting is scheduled for September 11.

~Julia

Gurwitz D, Fortier I, Lunshof JE, Knoppers BM. Research ethics: Children and population biobanks. Science. 2009 Aug 14; 325(5942):818-9

Hastings PJ, Lupski JR, Rosenberg SM, Ira G. Mechanisms of change in gene copy number. Nat Rev Genet. 2009 Aug; 10(8):551-64.

Holsinger KE, Weir BS. Genetics in geographically structured populations: defining, estimating and interpreting F(ST). Nat Rev Genet. 2009 Sep; 10(9):639-50.

Koga Y, Pelizzola M, Cheng E, Krauthammer M, Sznol M, Ariyan S, Narayan D, Molinaro AM, Halaban R, Weissman SM. Genome-wide screen of promoter methylation identifies novel markers in melanoma. Genome Res. 2009 Aug; 19(8):1462-70.

Monier A, Pagarete A, de Vargas C, Allen MJ, Read B, Claverie JM, Ogata H. Horizontal gene transfer of an entire metabolic pathway between a eukaryotic alga and its DNA virus. Genome Res. 2009 Aug; 19(8):1441-9.

Raveh-Sadka T, Levo M, Segal E. Incorporating nucleosomes into thermodynamic models of transcription regulation. Genome Res. 2009 Aug; 19(8):1480-96.

Rosenberg NA, Vanliere JM. Replication of genetic associations as pseudoreplication due to shared genealogy. Genet Epidemiol. 2009 Sep; 33(6):479-87.

Schmitz D, Netzer C, Henn W. An offer you can't refuse? Ethical implications of non-invasive prenatal diagnosis. Nat Rev Genet. 2009 Aug; 10(8):515.

Fundamental concepts in genetics: http://www.nature.com/nrg/series/fundamental/index.html

PCG Journal Club Articles, 7/31

Here are citations for the articles discussed at our most recent meeting (July 31). Our next meeting is scheduled for August 14.
~Julia

Bogdanowicz W, Allen M, Branicki W, Lembring M, Gajewska M, Kupiec T. Genetic identification of putative remains of the famous astronomer Nicolaus Copernicus. Proc Natl Acad Sci U S A, 2009 Jul 7 [Epub ahead of print].

Green RC, Roberts JS, Cupples LA, Relkin NR, Whitehouse PJ, Brown T, Eckert SL, Butson M, Sadovnick AD, Quaid KA, Chen C, Cook-Deegan R, Farrer LA; REVEAL Study Group. Disclosure of APOE genotype for risk of Alzheimer's disease. N Engl J Med, 2009 Jul 16; 361(3):245-54.

International Schizophrenia Consortium, Purcell SM, Wray NR, Stone JL, Visscher PM, O'Donovan MC, Sullivan PF, Sklar P. Common polygenic variation contributes to risk of schizophrenia and bipolar disorder. Nature, 2009 Aug 6; 460(7256):748-52.

Pevzner P, Shamir R. Computing has changed biology--biology education must catch up. Science, 2009 Jul 31; 325(5940):541-2. No abstract available.

Pomerantz MM, Ahmadiyeh N, Jia L, Herman P, Verzi MP, Doddapaneni H, Beckwith CA, Chan JA, Hills A, Davis M, Yao K, Kehoe SM, Lenz HJ, Haiman CA, Yan C, Henderson BE, Frenkel B, Barretina J, Bass A, Tabernero J, Baselga J, Regan MM, Manak JR, Shivdasani R, Coetzee GA, Freedman ML. The 8q24 cancer risk variant rs6983267 shows long-range interaction with MYC in colorectal cancer. Nat Genet, 2009 Aug; 41(8):882-4.

Rosser ZH, Balaresque P, Jobling MA. Gene conversion between the X chromosome and the male-specific region of the Y chromosome at a translocation hotspot. Am J Hum Genet, 2009 Jul; 85(1):130-4.

Tuupanen S, Turunen M, Lehtonen R, Hallikas O, Vanharanta S, Kivioja T, Björklund M, Wei G, Yan J, Niittymäki I, Mecklin JP, Järvinen H, Ristimäki A, Di-Bernardo M, East P, Carvajal-Carmona L, Houlston RS, Tomlinson I, Palin K, Ukkonen E, Karhu A, Taipale J, Aaltonen LA. The common colorectal cancer predisposition SNP rs6983267 at chromosome 8q24 confers potential to enhanced Wnt signaling. Nat Genet, 2009 Aug; 41(8):885-90. Epub 2009 Jun 28.

Wain LV, Armour JA, Tobin MD. Genomic copy number variation, human health, and disease. Lancet, 2009 Jul 25; 374(9686):340-50. Review.

PCG Journal Club Articles, 7/17

Here are citations for the articles discussed at our most recent meeting (July 17). Our next meeting is scheduled for July 31.
~Julia

Bianconi G, Pin P, Marsili M. Assessing the relevance of node features for network structure. Proc Natl Acad Sci U S A, 2009 Jul 14; 106(28):11433-8.

Briggs AW, Good JM, Green RE, Krause J, Maricic T, Stenzel U, Lalueza-Fox C, Rudan P, Brajkovic D, Kucan Z, Gusic I, Schmitz R, Doronichev VB, Golovanova LV, de la Rasilla M, Fortea J, Rosas A, Pääbo S. Targeted retrieval and analysis of five Neandertal mtDNA genomes. Science, 2009 Jul 17; 325(5938):318-21.

Cagliani R, Fumagalli M, Pozzoli U, Riva S, Comi GP, Torri F, Macciardi F, Bresolin N, Sironi M. Diverse evolutionary histories for beta-adrenoreceptor genes in humans. Am J Hum Genet, 2009 Jul; 85(1):64-75.

Elbers CC, van Eijk KR, Franke L, Mulder F, van der Schouw YT, Wijmenga C, Onland-Moret NC. Using genome-wide pathway analysis to unravel the etiology of complex diseases. Genet Epidemiol, 2009 Jul; 33(5):419-31.

Greenway SC, et al. De novo copy number variants identify new genes and loci in isolated sporadic tetralogy of Fallot. Nat Genet. 2009 Jul 13. [Epub ahead of print]

Hastings PJ, Lupski JR, Rosenberg SM, Ira G. Mechanisms of change in gene copy number. Nat Rev Genet, 2009 Aug; 10(8):551-64.

Holmans P, Green EK, Pahwa JS, Ferreira MA, Purcell SM, Sklar P; Wellcome Trust Case-Control Consortium, Owen MJ, O'Donovan MC, Craddock N. Gene ontology analysis of GWA study data sets provides insights into the biology of bipolar disorder. Am J Hum Genet, 2009 Jul; 85(1):13-24.

Huttenhower C, Haley EM, Hibbs MA, Dumeaux V, Barrett DR, Coller HA, Troyanskaya OG. Exploring the human genome with functional maps. Genome Res, 2009 Jun; 19(6):1093-106.

The International Schizophrenia Consortium. Common polygenic variation contributes to risk of schizophrenia and bipolar disorder. Nature, 2009 Jul 1. [Epub ahead of print]

Johannes F, Porcher E, Teixeira FK, Saliba-Colombani V, Simon M, Agier N, Bulski A, Albuisson J, Heredia F, Audigier P, Bouchez D, Dillmann C, Guerche P, Hospital F, Colot V. Assessing the impact of transgenerational epigenetic variation on complex traits. PLoS Genet, 2009 Jun; 5(6):e1000530.

Mendell JT. Tumors line up for a letdown. Nat Genet, 2009 Jul; 41(7):768-9.

Murphy A, Tantisira KG, Soto-Quirós ME, Avila L, Klanderman BJ, Lake S, Weiss ST, Celedón JC. PRKCA: a positional candidate gene for body mass index and asthma. Am J Hum Genet, 2009 Jul; 85(1):87-96.

Newcombe PJ, Verzilli C, Casas JP, Hingorani AD, Smeeth L, Whittaker JC. Multilocus Bayesian meta-analysis of gene-disease associations. Am J Hum Genet, 2009 May; 84(5):567-80.

Nicodemus KK, Malley JD. Predictor correlation impacts machine learning algorithms: implications for genomic studies. Bioinformatics, 2009 Aug 1; 25(15):1884-90.

Song M, Nicolae DL. Restricted parameter space models for testing gene-gene interaction. Genet Epidemiol, 2009 Jul; 33(5):386-93.

Spencer CC, Su Z, Donnelly P, Marchini J. Designing genome-wide association studies: sample size, power, imputation, and the choice of genotyping chip. PLoS Genet, 2009 May; 5(5):e1000477.

Vansteelandt S, Goetgeluk S, Lutz S, Waldman I, Lyon H, Schadt EE, Weiss ST, Lange C. On the adjustment for covariates in genetic association analysis: a novel, simple principle to infer direct causal effects. Genet Epidemiol, 2009 Jul; 33(5):394-405.

PCG Journal Club Articles, 6/24

Here are citations for the articles discussed at our most recent meeting (June 24). Our next meeting is scheduled for July 17.
~Julia

Choi Y, Wijsman EM, Weir BS. Case-control association testing in the presence of unknown relationships. Genet Epidemiol. 2009 Mar 30. [Epub ahead of print]

Gao X, Becker LC, Becker DM, Starmer JD, Province MA. Avoiding the high Bonferroni penalty in genome-wide association studies. Genet Epidemiol. 2009 May 11. [Epub ahead of print]

Hartge P. Genetics of reproductive lifespan. Nat Genet. 2009 Jun; 41(6): 637-8.

He C, Kraft P, Chen C, Buring JE, Paré G, Hankinson SE, Chanock SJ, Ridker PM, Hunter DJ, Chasman DI. Genome-wide association studies identify loci associated with age at menarche and age at natural menopause. Nat Genet. 2009 May 17. [Epub ahead of print]

Ong KK, et al. Genetic variation in LIN28B is associated with the timing of puberty. Nat Genet. 2009 May 17. [Epub ahead of print]

Perry JR, et al. Meta-analysis of genome-wide association data identifies two loci influencing age at menarche. Nat Genet. 2009 May 17. [Epub ahead of print]

Stolk L, et al. Loci at chromosomes 13, 19 and 20 influence age at natural menopause. Nat Genet. 2009 May 17. [Epub ahead of print]

Sulem P, et al. Genome-wide association study identifies sequence variants on 6q21 associated with age at menarche. Nat Genet. 2009 May 17. [Epub ahead of print]

PCG Journal Club Articles, 5/13 & 5/27

Hi! I'm Julia Wall, the Technical Writer in Vanderbilt's CHGR. Every two weeks or so, I'll be posting citation links to the articles that the students in our Program for Computational Genomics (PCG) Journal Club discuss in their bimonthly meetings. Enjoy!

PCG Journal Club Articles, 5/13

Baranzini SE, Galwey NW, Wang J, Khankhanian P, Lindberg R, Pelletier D, Wu W, Uitdehaag BM, Kappos L; GeneMSA Consortium, Polman CH, Matthews PM, Hauser SL, Gibson RA, Oksenberg JR, Barnes MR. Pathway and network-based analysis of genome-wide association studies in multiple sclerosis. Hum Mol Genet, 18(11):2078-90 (2009).

Stoddart D, Heron AJ, Mikhailova E, Maglia G, Bayley H. Single-nucleotide discrimination in immobilized DNA oligonucleotides with a biological nanopore. Proc Natl Acad Sci USA, 106(19):7702-7 (2009).

PCG Journal Club Articles, 5/27

Barrett JC, Clayton DG, Concannon P, Akolkar B, Cooper JD, Erlich HA, Julier C, Morahan G, Nerup J, Nierras C, Plagnol V, Pociot F, Schuilenburg H, Smyth DJ, Stevens H, Todd JA, Walker NM, Rich SS; The Type 1 Diabetes Genetics Consortium. Genome-wide association study and meta-analysis find that over 40 loci affect risk of type 1 diabetes. Nature Genetics, 2009 May 10 [Epub ahead of print].

Biswas S, Scheinfeldt LB, Akey JM. Genome-wide insights into the patterns and determinants of fine-scale population structure in humans. AJHG, 84(5): 641-50 (2009).

Glessner JT, Wang K, Cai G, Korvatska O, Kim CE, Wood S, Zhang H, Estes A, Brune CW, Bradfield JP, Imielinski M, Frackelton EC, Reichert J, Crawford EL, Munson J, Sleiman PM, Chiavacci R, Annaiah K, Thomas K, Hou C, Glaberson W, Flory J, Otieno F, Garris M, Soorya L, Klei L, Piven J, Meyer KJ, Anagnostou E, Sakurai T, Game RM, Rudd DS, Zurawiecki D, McDougle CJ, Davis LK, Miller J, Posey DJ, Michaels S, Kolevzon A, Silverman JM, Bernier R, Levy SE, Schultz RT, Dawson G, Owley T, McMahon WM, Wassink TH, Sweeney JA, Nurnberger JI, Coon H, Sutcliffe JS, Minshew NJ, Grant SF, Bucan M, Cook EH, Buxbaum JD, Devlin B, Schellenberg GD, Hakonarson H. Autism genome-wide copy number variation reveals ubiquitin and neuronal genes. Nature, 2009 April 28 [Epub ahead of print].

Ioannidis JP, Thomas G, Daly MJ. Validating, augmenting and refining genome-wide association signals. Nat Rev Genet, 10(5): 318-29 (2009).

Newcombe PJ, Verzilli C, Casas JP, Hingorani AD, Smeeth L, Whittaker JC. Multilocus Bayesian meta-analysis of gene-disease associations. AJHG, 84(5): 567-80 (2009).

Spencer SL, Gaudet S, Albeck JG, Burke JM, Sorger PK. Non-genetic origins of cell-to-cell variability in TRAIL-induced apoptosis. Nature, 459(7245): 428-32 (2009).

Thomas A, Camp NJ, Farnham J, Allen-Brady K, Cannon-Albright LA. Shared genomic segment analysis. Mapping disease predisposition genes in extended pedigrees using SNP genotype assays. Ann Hum Genet, 72(Pt2): 279-87 (2008).

Yoshida Y, Makita Y, Heida N, Asano S, Matsushima A, Ishii M, Mochizuki Y, Masuya H, Wakana S, Kobayashi N, Toyoda T. PosMed (Positional Medline): prioritizing genes with an artificial neural network comprising medical documents to accelerate positional cloning. Nucleic Acids Res, 2009 May 25 [Epub ahead of print].

Journal club notes coming soon

The Program in Computational Genomics holds a journal club twice a month. Our technical writer Julia Wall will soon start posting here references to the articles we talked about. Keep an eye out here to see some of the latest research we're discussing!