Next Generation Sequencing A paradigm shift practice with

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 • 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)

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

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

Sanger vs. NGS Sanger sequencing next generation sequencing

Analyzing the clinical significance of the variants

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

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

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

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

448 severe recessive childhood diseases 7717 regions from 437 target genes 93% of target nucleotide with >20 X coverage ~95% sensitivity ~100% specificity 104 samples tested Average carrier burden 2. 8 (0 -7)