Tools in Human Genomics

Brett BowmanMarch 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 bp with 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 vs Exome

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 SequencingHow many human genomes have been

completely sequenced end-to-end?

Full Genome SequencingHow 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

SNPedia - Promethease

openSNP

OMIM

23andMe API

Genomes Unzipped

Questions?