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1000 Genomes SV detection Boston College. Chip Stewart 24 November 2008. Spanner: RP approach. Paired-end SV breakpoint detection Detect clusters of fragments spanning breakpoints Classify clusters into SV types Estimate CN from read counts in candidate region. Pattern:

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1000 genomes sv detection boston college

1000 Genomes SV detectionBoston College

Chip Stewart

24 November 2008

spanner rp approach
Spanner: RP approach

Paired-end SV breakpoint detection

  • Detect clusters of fragments spanning breakpoints
  • Classify clusters into SV types
  • Estimate CN from read counts in candidate region

Pattern:

PE RD

DNA

REFERENCE

LF

LM

LM ~ LF + Ldel low coverage

deletion

Ldel

tandemduplication

LM~ LF – Ldup high coverage

Ldup

LM

LM~ +LinvLM ~ -Linv normal coverage

ends flipped

inversion

Linv

Spanner / BC

spanner rd approach
Spanner … RD approach

Read Depth Copy Number Variation (CNV) detection

  • Count uniquely aligned reads in windows (1kb) across chromosomes.
  • Correct for micro-repeat artifact with an “alignabilty” metric to estimate expected number of uniquely aligned reads in each window. Local copy number is based on the likelihood that the estimated count of reads scaled by copy number will fluctuate (Poisson) to the observed count.
  • Identify CN breakpoints (this is still in the works)

Alignability:

Define “alignabilty” for a given chromosome position as:

This becomes tractable when considering a random sample of possible reads within a window of positions.

Spanner / BC

alignabilty
Alignabilty

Coverage profiles from NA12878 for a 1.2MB region of chromosome 4.

Reads/1kb

The count of unique aligned read (up to 4 mismatches) in non-overlapping windows of 1kb. compared with the expected count of reads based on A(p).

expected Reads/1kb

Chromosome 4 position [Mb]

Reads/1kb

A(p) has a 90% correlation with observed read coverage variance.

Position [Mb]

expected Reads/1kb

Spanner / BC

sv event display matlab tool
SV event display matlab tool

300bp ALU deletion in chromosome 1 of NA12878

chromosome

overview

fragment lengths

readdepth

eventtrack

Spanner / BC

tandem duplication event
Tandem duplication event
  • NA12878 chromosome 1

Spanner / BC

complex sv
“Complex” SV
  • NA12878 chromosome 8

Spanner / BC