Table 4.
Sequencing details for seven large genome-scale studies
| Study type | Exome (research study) | Exome (clinical laboratory) | Genome | ||||
|---|---|---|---|---|---|---|---|
| Study | Zhu et al. (136) | NCGENESa | Lee et al. (68) | Yang et al. (134) | Farwell et al. (39) | Retterer et al. (99) | Taylor et al. (120) |
| Capture | Illumina TruSeq Exome Enrichment kit (65 Mb) Roche NimbleGen SeqCap EZ Human Exome Library kit Agilent SureSelect Human All Exon kit (50 Mb) |
Agilent SureSelectXT | Customized Agilent SureSelect Human All Exon V2 kit (50 Mb) | Roche NimbleGen SeqCap EZ HGSC VCRome (version 2.1) | Agilent SureSelect Target Enrichment System Roche NimbleGen SeqCap EZ HGSC VCRome (version 2.0) |
Agilent SureSelect Human All Exon V4 kit (50 Mb) | None |
| Sequencing platform | Illumina HiSeq 2000 | Illumina HiSeq 2000 and 2500 | Illumina HiSeq 2000 (50 bp paired-end) or 2500 (100 bp paired-end) | Illumina Genome Analyzer IIx (100 bp paired-end) or HiSeq 2000 | Not specified | Illumina HiSeq 2000 or 2500 (100 bp paired-end) | Illumina HiSeq 2000 or 2500 (100 bp) |
| Alignment software | BWA (version 0.5.10) | BWA | NovoAlign (version 2.07.15b) GATK (version 1.1-33) |
BWA (version 0.5.10) | Not specified | BWA | BWA (version 0.5.6) Stampy (versions 1.0.12–1.0.22) |
| Variant caller | GATK (version 1.6-11) Annotation SnpEff (version 3.3) |
GATK | VAX | Internal annotation databases | CASAVA Pindel |
SAMtools (version 0.1.18) | Platypus (version 0.1.9) |
| Minimum coverage | 10x | 30x | 10x | 20x | 10x | 10x | 22x |
| Variant filtering | Allele frequency, inheritance pattern, variant type, coverage, and quality score | Disease-based gene lists, allele frequency, variant type, coverage, and quality score | MySQL 5.2 database for filtering by variant type and MAF (analyzing variants with a MAF of <1%) | Cassandra (BCM software) | Stepwise filtering by variant type, MAF, and family history using the FIND bioinformatics program | Phenotype-driven gene lists (HPO and HGMD), inheritance patterns, variant type, phenotype, and population frequencies | Variant functional impact, frequency in the population, inheritance patterns and, statistical evidence for association (when applicable) |
Abbreviations: bp, base pair; BWA, Burrows-Wheeler Aligner; CASAVA, Consensus Assessment of Sequence and Variation; FIND, Family History Inheritance-Based Detection; GATK, Genome Analysis Toolkit; HGMD, Human Gene Mutation Database; HPO, Human Phenotype Ontology; MAF, minor allele frequency; NA, not applicable; NCGENES, North Carolina Clinical Genomic Evaluation by Next-Generation Exome Sequencing; VAX, Variant Annotator X.
a
J.S. Berg, N.T. Strande, G. Haskell, B. Powell, A.K.M. Foreman, et al., manuscript in preparation.