Caveats: I have not taken notes in every talk of every session, a lack of notes for a particular speaker does not constitute disinterest on my part, I simply took notes for the talks that were directly related to my current work. If I have misquoted, misrepresented or misunderstood anything, and you are the speaker concerned, or a member of the team involved in the work, please leave a comment on the post, and I will rectify the situation accordingly.
7.1 Christine Eng, Baylor College of Medicine: “Clinical Exome Sequencing for the Diagnosis of Mendelian Disorders”
Christine spoke about the pipeline for clinical WES at Baylor. Samples are sequenced to 140x to achieve 85%>40x coverage for the exome. A SNP array is run in conjunction with each sample. Concordance with the SNP array is tested for each sample and this must exceed 99%.
BWA is the primary mapper, but variants are called with ATLAS and annotated with Cassandra (Annovar is a dependency of Cassandra)
Critical resource: https://www.hgsc.bcm.edu/software/cassandra
Critical resource: http://sourceforge.net/projects/atlas2/
Critical paper: http://genome.cshlp.org/content/20/2/273.short “A SNP discovery method to assess variant allele probability from next-generation resequencing data”
Variants are filtered against HGMD. Filtered for variants which are <5% MAF. 4000 clinical internal exomes have been run so there is a further requirement for variants to have a <2% MAF in this dataset.
New gene list is updated for the system weekly and VOUS are reported in genes related to the disorder to all patients – this is much more extensive reporting than for those groups who feel VOUS muddy the waters.
An expanded report can be requested in addition which also reports deleterious mutations in genes for which there is no disease/phenotype linkage. The hit rate for molecular diagnostics via clinical exome is 25% and 75% are not clinically solved. These are then asked if they would like to opt in to a research programme so that the data can be shared and aggregated for greater diagnostic power.
11/504 cases had two distinct disorders presenting at the same time. 280 cases were autosomal dominant and 86% of the dominant cases are de novo mutations. 187 cases were autosomal recessive and this was 57% compound heterozygous, 3% UPD and 37% had homozygosity due to shared ancestry.
Many initially unsolved diagnoses can be revisited and successfully resolved 6-12 months later on revisiting the data such is the base of new data deposition.
They use guidelines from CPIC (from PharmGKB) and data on drug/gene interactions and there is linking to a prescription database, so the pipeline is ‘end to end’.
Critical resource: http://www.pharmgkb.org/page/cpic