Accurate and comprehensive sequencing of personal genomes

作者：Ajay Subramanian S; Parker Stephen C J; Abaan Hatice Ozel; Fajardo Karin V Fuentes; Margulies Elliott H^*

来源：Genome Research, 2011, 21(9): 1498-1505.

DOI：10.1101/gr.123638.111

As whole-genome sequencing becomes commoditized and we begin to sequence and analyze personal genomes for clinical and diagnostic purposes, it is necessary to understand what constitutes a complete sequencing experiment for determining genotypes and detecting single-nucleotide variants. Here, we show that the current recommendation of similar to 30x coverage is not adequate to produce genotype calls across a large fraction of the genome with acceptably low error rates. Our results are based on analyses of a clinical sample sequenced on two related Illumina platforms, GAII(x) and HiSeq 2000, to a very high depth (126x). We used these data to establish genotype-calling filters that dramatically increase accuracy. We also empirically determined how the callable portion of the genome varies as a function of the amount of sequence data used. These results help provide a "sequencing guide'' for future whole-genome sequencing decisions and metrics by which coverage statistics should be reported.

• 出版日期2011-9