cancer ngs - research / clinic bioinformatics challenges

CANCER NGS - RESEARCH / CLINIC
BIOINFORMATICS CHALLENGES
Anthony Ferrari
Plateforme Bioinformatique
Synergie Lyon Cancer
« Grant INCa-4664 »
www.cancer-lyric.com
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NGS FAST EVOLUTION
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2005
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PROGRAMS
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  HER2+ Amplified Breast Cancer
(G. Thomas, A. Viari)
  75 genome pairs, Tumour 45x, Normal 30x
  RNA-seq Infinium 450k
  Prostate Cancer
(O. Cussenot)
  25 genome pairs, Tumour 45x, Normal 30x
  RNA-seq
Exomes
Gynecological Carcinosarcoma
(A. Puisieux)
  20 genome pairs, Tumour 75x, Normal 50x
  RNA-seq
Infinium 450k
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INFRASTRUCTURES
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WHOLE GENOME – TUMOUR 50X, NORMAL 30X
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INFRASTRUCTURES
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  INCa – Synergie cluster
  64 computing nodes [ 8 cpus // 64Gb RAM ]
  400Tb effective storage
  LYRIC cluster
  20 computing nodes [ 12 cpus // 128Gb RAM ]
  100Tb effective storage + 60Tb backup storage.
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QUALITY CONTROLS
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GENOMIC ALTERATIONS
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VARIANTS STRUCTURAUX
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SUMMARY
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  Importance of infrastructure & data management
  SNV
  Good concordance
  No best pipeline though
Indels
  Very weak concordance
  Improvements required
  Structural variants
  Systematic detection is difficult
  False positives
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MORE CHALLENGES
« Grant INCa-4664 »
  Tumour heterogeneity, subclones
  Non coding DNA role in tumorigenesis
  Data analyses integration
 
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REMERCIEMENTS
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