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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

Next Generation Sequencing

A paradigm shift practice with great opportunity and challenge

next generation sequencing1
Next Generation Sequencing
  • What can NGS do:
    • Detects nucleotide substitution
    • Detects indel
    • Detects CNV
    • Detects translocation
    • Detects inversion
    • Detects methylation
next generation sequencing2
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
Examples of NGS platforms

100Mb $500 100bp/reads

slide5

Mi-Seq

1-1.5Gb $1200 150bp/run

sanger vs ngs
Sanger vs. NGS

Sanger sequencing next generation sequencing

vast array of genetic disorders
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
Variant categorization
  • Known deleterious (condition relevant and incidental)
  • Presumed deleterious
  • VUS (variants of undetermined significance)
  • Presumed benign
  • Known benign
reportability
Reportability
  • Clinically actionable--YES
  • Clinically valid but not actionable--YES/NO
  • Unknown or no clinical significance—NO
  • Presumed benign/known benign--NO
counseling
Counseling
  • Pre-test
  • Post-test
  • Update
  • Who gets the test? Who should know the results? (part of the results or all)
slide12

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)