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Best practices and joint calling of the HumanExome BeadChip: the CHARGE Consortium.
Monday,2013-09-30 16:52 America/Los_Angeles — poolea2
| Title | Best practices and joint calling of the HumanExome BeadChip: the CHARGE Consortium. |
| Publication Type | Journal Article |
| Year of Publication | 2013 |
| Authors | Grove, ML, Yu, B, Cochran, BJ, Haritunians, T, Bis, JC, Taylor, KD, Hansen, M, Borecki, IB, Cupples, AL, Fornage, M, Gudnason, V, Harris, TB, Kathiresan, S, Kraaij, R, Launer, LJ, Levy, D, Liu, Y, Mosley, T, Peloso, GM, Psaty, BM, Rich, SS, Rivadeneira, F, Siscovick, DS, Smith, AV, Uitterlinden, A, van Duijn, CM, Wilson, JG, O'Donnell, CJ, Rotter, JI, Boerwinkle, E |
| Journal | PLoS One |
| Volume | 8 |
| Issue | 7 |
| Pagination | e68095 |
| Date Published | 2013 |
| ISSN | 1932-6203 |
| Keywords | Aging, Alleles, Cluster Analysis, Cohort Studies, Continental Population Groups, Exome, Female, Gene Frequency, Genomics, Genotype, Heart, Humans, Male, Oligonucleotide Array Sequence Analysis, Polymorphism, Single Nucleotide, Sample Size, Self Report, Sequence Analysis, DNA |
| Abstract | <p>Genotyping arrays are a cost effective approach when typing previously-identified genetic polymorphisms in large numbers of samples. One limitation of genotyping arrays with rare variants (e.g., minor allele frequency [MAF] <0.01) is the difficulty that automated clustering algorithms have to accurately detect and assign genotype calls. Combining intensity data from large numbers of samples may increase the ability to accurately call the genotypes of rare variants. Approximately 62,000 ethnically diverse samples from eleven Cohorts for Heart and Aging Research in Genomic Epidemiology (CHARGE) Consortium cohorts were genotyped with the Illumina HumanExome BeadChip across seven genotyping centers. The raw data files for the samples were assembled into a single project for joint calling. To assess the quality of the joint calling, concordance of genotypes in a subset of individuals having both exome chip and exome sequence data was analyzed. After exclusion of low performing SNPs on the exome chip and non-overlap of SNPs derived from sequence data, genotypes of 185,119 variants (11,356 were monomorphic) were compared in 530 individuals that had whole exome sequence data. A total of 98,113,070 pairs of genotypes were tested and 99.77% were concordant, 0.14% had missing data, and 0.09% were discordant. We report that joint calling allows the ability to accurately genotype rare variation using array technology when large sample sizes are available and best practices are followed. The cluster file from this experiment is available at www.chargeconsortium.com/main/exomechip. </p> |
| DOI | 10.1371/journal.pone.0068095 |
| Alternate Journal | PLoS ONE |
| PubMed ID | 23874508 |
| PubMed Central ID | PMC3709915 |
| Grant List | N01-HC-25195 / HC / NHLBI NIH HHS / United States U01 HL56565 / HL / NHLBI NIH HHS / United States N01-HC-45205 / HC / NHLBI NIH HHS / United States R01-HL-071258, , / HL / NHLBI NIH HHS / United States N01-HC-95162 / HC / NHLBI NIH HHS / United States UL1TR000124 / TR / NCATS NIH HHS / United States N01-HC-05187 / HC / NHLBI NIH HHS / United States R01-HL-071252 / HL / NHLBI NIH HHS / United States 5RC2HL102419 / HL / NHLBI NIH HHS / United States N01 HC-95171 / HC / NHLBI NIH HHS / United States U01 HL56564 / HL / NHLBI NIH HHS / United States HHSN2682011000010C / / PHS HHS / United States UL1-RR-025005 / RR / NCRR NIH HHS / United States N01-HC-48047 / HC / NHLBI NIH HHS / United States HHSN268201100005C / / PHS HHS / United States HL105756 / HL / NHLBI NIH HHS / United States N01AG62101 / AG / NIA NIH HHS / United States N01-HC-95163 / HC / NHLBI NIH HHS / United States R01-HL-071250 / HL / NHLBI NIH HHS / United States N01-HC-95168 / HC / NHLBI NIH HHS / United States UL1-RR-024156 / RR / NCRR NIH HHS / United States AG-15928 / AG / NIA NIH HHS / United States U01 HL56566 / HL / NHLBI NIH HHS / United States HHSN268201100009C / / PHS HHS / United States N01-HC-45204 / HC / NHLBI NIH HHS / United States N01-HC-95159 / HC / NHLBI NIH HHS / United States 1R01AG032098-01A1 / AG / NIA NIH HHS / United States DK-35816 / DK / NIDDK NIH HHS / United States N01-HC-95095 / HC / NHLBI NIH HHS / United States N01-HC-95165 / HC / NHLBI NIH HHS / United States HL087652 / HL / NHLBI NIH HHS / United States UL1 TR000124 / TR / NCATS NIH HHS / United States U01 HL56569 / HL / NHLBI NIH HHS / United States R01-HL-071251 / HL / NHLBI NIH HHS / United States R01-HL-084099 / HL / NHLBI NIH HHS / United States N01-HC-85086 / HC / NHLBI NIH HHS / United States N01-HC-48050 / HC / NHLBI NIH HHS / United States AG-027058 / AG / NIA NIH HHS / United States N01-HC-35129 / HC / NHLBI NIH HHS / United States N01-HC-45134 / HC / NHLBI NIH HHS / United States N01 HC-55222 / HC / NHLBI NIH HHS / United States HL41993 / HL / NHLBI NIH HHS / United States HHSN268201100008C / / PHS HHS / United States R01-HL-071259 / HL / NHLBI NIH HHS / United States N01-HC-95169 / HC / NHLBI NIH HHS / United States N01-HC-95164 / HC / NHLBI NIH HHS / United States R01-HL-071205 / HL / NHLBI NIH HHS / United States N01-HC-48049 / HC / NHLBI NIH HHS / United States N01 HC-95172 / HC / NHLBI NIH HHS / United States N01-HC-75150 / HC / NHLBI NIH HHS / United States HHSN2682011000012C / / PHS HHS / United States N01-HC-95160 / HC / NHLBI NIH HHS / United States N01 HC-15103 / HC / NHLBI NIH HHS / United States U01 HL56568 / HL / NHLBI NIH HHS / United States HHSN268201100007C / / PHS HHS / United States P30 DK035816 / DK / NIDDK NIH HHS / United States U01-HG-004729 / HG / NHGRI NIH HHS / United States U01 HL56567 / HL / NHLBI NIH HHS / United States N01-AG-12100 / AG / NIA NIH HHS / United States DK063491 / DK / NIDDK NIH HHS / United States N01-HC-45133 / HC / NHLBI NIH HHS / United States K01-HL70444 / HL / NHLBI NIH HHS / United States N01-HC-85079 / HC / NHLBI NIH HHS / United States N01-HC-95161 / HC / NHLBI NIH HHS / United States N01AG62103 / AG / NIA NIH HHS / United States HHSN268201200036C / / PHS HHS / United States U01 HL56563 / HL / NHLBI NIH HHS / United States HL080295 / HL / NHLBI NIH HHS / United States N01AG62106 / AG / NIA NIH HHS / United States N01-HC-85239 / HC / NHLBI NIH HHS / United States N01-HC-48048 / HC / NHLBI NIH HHS / United States AG-023629 / AG / NIA NIH HHS / United States HHSN268201100006C / / PHS HHS / United States R01- HL-071051 / HL / NHLBI NIH HHS / United States N01-HC-95166 / HC / NHLBI NIH HHS / United States HL091244 / HL / NHLBI NIH HHS / United States N01 HC-95170 / HC / NHLBI NIH HHS / United States N01-HC-95167 / HC / NHLBI NIH HHS / United States HHSN2682011000011C / / PHS HHS / United States |