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Copy Number Alterations with Massively Parallel Sequencing

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Copy Number Alterations with Massively Parallel Sequencing

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    1. Copy Number Alterations with Massively Parallel Sequencing Presented By Robert Shields Case Western Reserve University June 3rd, 2009

    2. Motivation Identify differences in copy number variation between normal and cancer cells

    3. Copy Number Ratio Partition the genome into windows of length L L (10kb – 100kb) Look at copy number ratios in each window

    4. Statistical Power of Fixed Window Need ~15 million aligned reads to detect one gain Need ~6 million aligned reads to detect one loss

    5. SegSeq – Step One Step One: Identify Possible Break Points D : Difference in ratios from two adjacent windows W : number of consecutive reads from normal sample

    6. SegSeq – Step One

    7. SegSeq – Step Two Calculate P-values of potential break points based on number of tumor reads

    8. SegSeq – Step Two If the Pvalue < Pinit we keep it as a candidate break point

    9. SegSeq – Step Three If the Pvalue > Pmerge we merge the segments Calculate P values on newly formed segments

    10. Comparing the Steps

    11. Sensitivity to Gain and Loss

    12. Results

    13. Results

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