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Next Generation Sequencing

Next Generation Sequencing. A paradigm shift practice with great opportunity and challenge. Next Generation Sequencing. What can NGS do: Detects nucleotide substitution Detects indel Detects CNV Detects translocation Detects inversion Detects methylation …. Next Generation Sequencing.

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Next Generation Sequencing

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  1. Next Generation Sequencing A paradigm shift practice with great opportunity and challenge

  2. Next Generation Sequencing • What can NGS do: • Detects nucleotide substitution • Detects indel • Detects CNV • Detects translocation • Detects inversion • Detects methylation • …

  3. Next Generation Sequencing • What are involved to do NGS: • Panel design and target capture • Bar-coding for multiplexing • Sequencing (choices of platform) • Informatics infrastructure • Sequence data analysis pipelines • Data (Variant interpretation)

  4. Examples of NGS platforms 100Mb $500 100bp/reads

  5. Mi-Seq 1-1.5Gb $1200 150bp/run

  6. Sanger vs. NGS Sanger sequencing next generation sequencing

  7. Analyzing the clinical significance of the variants

  8. VAST ARRAY OF GENETIC DISORDERS Chromosomal Trisomies, aneuploidies, etc. Metabolic SLO, CDG, many others Organ Specific Cardiopathies, GI, Renal Protein DMD, Huntington, Immunoglobulins Cancer At risk mutations And On and On

  9. Variant categorization • Known deleterious (condition relevant and incidental) • Presumed deleterious • VUS (variants of undetermined significance) • Presumed benign • Known benign

  10. Reportability • Clinically actionable--YES • Clinically valid but not actionable--YES/NO • Unknown or no clinical significance—NO • Presumed benign/known benign--NO

  11. Counseling • Pre-test • Post-test • Update • Who gets the test? Who should know the results? (part of the results or all) • …

  12. 448 severe recessive childhood diseases 7717 regions from 437 target genes 93% of target nucleotide with >20X coverage ~95% sensitivity ~100% specificity 104 samples tested Average carrier burden 2.8 (0-7)

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