Measurements for Reference Material Characterization Working Group Summary Aug2012
Measurements for Reference Material Characteriza4on Develop a consensus plan for experimental characteriza4on of Reference Materials Genome in a Bo;le Working Group
Determine library prepara4on protocols • Fosmid and/or a BAC library? • Need to keep some cells for plaGorm-‐speciﬁc DNA puriﬁca4on needs (e.g., to get high-‐ molecular-‐weight DNA) • Include sequencing family members
Determine sequencing plaGorms • Illumina – 300-‐600bp inserts – 3ish kb mate-‐pair – 2x100bp reads on HiSeq • PacBio – >10kbish inserts – 1x90m “movies” – Who will do it and pay for it? – PacBio may be able to create the libraries – Chris Mason to sequence? • Life Tech – 5500 data at NIST (1,6, and 10kb mate pairs) – Ion Torrent/Proton data (who to generate?) • Complete – Standard libraries and LFR approach – Start with cells • 454? – 700-‐800bp reads? • Newer technologies – are they used for veriﬁca4on/valida4on only? – Oxford Nanopore? – GnuBio?
“Error Correc4on” and Veriﬁca4on (not valida4on) • ArrayCGH and SNP Chip • OpGen (or other op4cal mapping approaches) • Targeted sequencing
Diﬃcult to sequence regions • Characterize MHC regions? – Use 454? • Other parts of the genome? • Approved CLIA-‐cer4ﬁed speciﬁc tests? – Highly mul4plexed TaqMan/Sanger style assay • CLIA-‐cer4ﬁed whole exome data • Do we pick very speciﬁc well-‐characterized fosmids?
Old vs New Data • What new data will we need to generate on the actual reference sample? • Can we use data that currently exists? • Or generate data now or vanilla Coriell samples?
Other Thoughts • BAC by BAC approach? • Divide the genome into the easy, medium, and hard bits – Easy = same call all the 4me on every plaGorm • How do we account for technological/ algorithmic improvements?