Genetic Cancer Susceptibility (GCS) Genomics in I4C James McKay

GCS aims and focus I.Identify and understand genetic susceptibility to cancer applying cutting edge genomics techniques to the large bio- repositories within GEN lung, head and neck, kidney cancers and lymphomas II. Genetics Platform (GSP) Develop and maintain genotyping / genomic applications Including the related bioinformatics

GCS studies Cancers prioritized by IARC GWAS – lung, hodgkin’s lymphoma, UADT cancers Pedigree analysis – Exome sequencing in unusual pedigrees NPC cancers in Sarawak, Malaysia, Bladder Cancer in Iran Novel strategies. Use an intregrative approach to maximise our ability to perform meaningful studies within limited sample sets ( mutation profiles, loss of second copy of alleles. eQTL)

Bidayuh NPC pedigree Kuching Sarawak Malaysia Pedigree in a loose sense, three isolated villages Discovery Exome sequencing + linkage analysis (snp arrays) Assess for segregation Validation Screening candidate genes in additional cases

Genetics platform Flexibility, suitability to IARC studies and bioropositories Next generation sequencing LifeTechnology 5500 and PGM Illumina bead array High performance computer cluster Highly dynamic field, what possible this week, needs to be revised next week

Rapid and cheap comprehensive sequencing of many tumours is only now becoming feasible 72.8 €/sample 12.2 €/sample  X 6 cost through GCS optimization Targeted Resequencing Ion Torrent Experiment Cost (35 amplicons, 150X coverage) Exome/Genome Sequencing Many genes/Few samples Targeted Resequencing Few genes/Many samples

Genes mutated within HNC Stransky N et al (2011). Science Within 100 (TCGA) head and neck tumours, 95% mutations reported within 10 genes. It becomes possible to design targeted sequencing assays to cover most mutations, and at low cost. Mutations can be detected in the DNA from plasma (0.1-1%)

Highly multiplexed PCR used for enrichment. Targeted combined amplification of genes up to amplicons/PCR 5 genes >240,000 amplicons whole exomes Using this to resequence candidate genes. 20 euros/sequence five genes. Applied to circulate tumour DNA (10,000X) to capture rare events Qaigen Generead

I4C genomics applications TEL/AML translocations What is there prevalence at birth (1% or 0.1%?). Dosage? Is presence of TEL/AML translocations predictive of ALL later in life? Is there a relationship between TEL/AML dose/patient and ALL? Is modified by other factors? Birthweight, age of onset (early ALL cases), gender…

TEL/AML translocation assayed using RNA Limitation is the availability of appropriate bio-specimens

A Zelent et al, Oncogene (2004) DNA assay for TEL/AML translocation Complicated as the breakpoint for the translocations is the variable. Complicated as the breakpoint for the translocations is the variable.

TEL (ETV6) gene 12 kb AML1 (RUNX1) gene 100 kb Tiled highly multiplexed PCR Low strigency PCR, coupled with very deep sequencing (10,000) to capture very rare variants N=60 (200bp) N=500 (200bp)