Download 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 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
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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
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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?
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?