Tools in Human Genomics

Tools in Human Genomics Brett Bowman March 3rd, 2013

Summary • Brief Bio • Review of Genotyping Technologies • SNP-chips (23andMe) • Exome Sequencing (In Clinical Use) • Whole Genome Sequencing • Review of SNP Analysis tools • SNP Databases • Report Tools • OMIM

My (Sort of) Karyotype

Genotyping TECHNOLOGIES

23andMe – How They Do It

23andMe – How it Works • Attach un-labeled sequence probes to array surface • Extract and Amplify sample DNA • Fragment • Wash over and bind to array probes • Extend probe 1 bpwith polymerase and labeled dNTPs • Photograph!

23andMe – Processed Output • rsid == refSNP id == dbSNP id • Two letter genotype representing both alleles • NOT phased data • No quality information

SNP-Chips Limitations • Requires a priori knowledge of SNPs of interest • Requires individual probes be designed and manufactured for each SNP • SNP-Chips limited by size in the number of probes they can contain • Cannot determine phase • Cannot determine copy number • Small Error Rate * Large Number = High Error Count

Exome Sequencing – How it Works • Prepare labeled sequence probes • Extract, Sheer, and clean-up DNA • Mix probes with DNA • Wash away un-bound DNA • Digest probes • Sequence!

Exome Sequencing – Raw Output

PHRED Quality Scores Encoded Score (E) = chr(Q + 33) Numerical Score (Q) = ord(E) - 33

Exome Sequencing – Processed Output

Exome Sequencing Limitations • Requires a priori knowledge of Genes of interest • Requires individual probes be designed and manufactured for each exon/gene • Hard to infer copy number • Very limited ability to phase data • Hard to make sense of novel data • Contains very little regulatory data • Complicated, unstandardized, computationally intensive analysis processes

SNP-Chip vsExome SNP-Chip • Cheaper (~$100) • Lower Accuracy • Requires precise knowledge a priori • At best gets 10-20% of known variants • No phasing data • No structural data • Simple analysis tools Exome • Expensive (~$1000) • Higher Accuracy • Requires general knowledge a priori • At best gets 80-90% of known variants • Some phasing data • Some structural data • Complex analysis tools

Full Genome Sequencing How many human genomes have been completely sequenced end-to-end?

Full Genome Sequencing How many human genomes have been completely sequenced end-to-end? 0

Full Genome Sequencing - Challenges • Sequence Repeats • Secondary Structure • Particularly • Telemeric Region • Centromeric Region • Methylation • Regulation • Interpretation

Analysis Tools

SNPedia

SNPedia - Promethease

openSNP

OMIM

23andMe API

Genomes Unzipped

Questions?

Tools in Human Genomics

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