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The genomic and transcriptomic architecture of 2,000 breast tumours reveals novel subgroups #
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주요 내용 #

Breast cancer와 관련된 Genomic (CNV) Transcriptomic (Gene expression) 유전자변화 종합 분석하고, 그룹화

This data are shared on behalf of METABRIC.

A breast cancer population genomic resource #

Genome variation affects tumor expression architecture #

Expression outliers refine the breast cancer landscape #

Trnas-acting association reveal distinct modules #

Integrative clustering reveals novel subgroups #

Pathway deregulation in the integrative subgroups #

Discussion #

Supplement #

8. Segmentation and copy number alteration calling using CBS #

Normalisation of intensities #

Genome-Wide Human SNP Array 6.0 데이터는 aroma.affymetrix를 써서 normal, tumor 각각 독립적으로 정규화함 (Copy-number estimation using Robust Multichip Analysis (CRMAv2)) - 270 HapMap 데이터 포함.

각각의 샘플에 대해

  1. allelic-crosstalk calibration
  2. probe sequence effects normalisation
  3. probe-level summarisation
  4. PCR fragment length normalisation

을 수행하고, log2 intensity 값들을 얻음. 그리고 이어서,

  1. genomic position에 따라 probe 정렬
  2. replicate probes는 median 값으로 요약
  3. missing values는 snapCGH의 loess procedure로 impute
  4. QC metrics
    • normalised unscaled standard error
    • relative log expression
    • signal-to-noise ratio of the log2 intensity data

Two pooled references

  1. median intensities across the MapMap individuals
  2. normal/tumour median intensity values (473 normals)

Calling of copy number alterations and adjustment for tumour cellularity #

DNAcopy 470 normals and 270 HapMap samples

DNAcopy Tomour samples, MergeLevels algorithm

Somatic copy number states:

$$ K_{CNA} = \{HOMD, HETD, NEUT, GAIN, AMP\} $$

Identification of germline CNVs #

$$ K_{CNA} = \{CNVLOSS, CNVGAIN\} $$

Gene-centric alterations #

Probe-level alterations #

Measures of genomic instability #

Identification of recurrent alterations #

9. Segmentation and copy number alteration calling using HMM #

Normalisation of intensities #

6-state HMM for segmentation and discrete copy number prediction in normals #

HMM-Dosage for segmentation and discrete copy number prediction in tumors #

Gene-centric alterations #

10. Comparison of segmentation methods based on MPLA #

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