SÃ

O P

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LO20

1820

18COURSE of NGS

...in a Diagnostics

Introduction; NGS terminology, types of variants 

Characteristics of the NGS sequencing methods (Illumina, Ion

Torrent, SOLiD, Pacific Biosciences, ...) 

Making the DNA sequence-ready, Quality Assurance,guidelines

for diagnostics NGS (based on the 3Gb-TEST papers of Matthijs

et al. (EJHG, WES) and White et al. (HumMut, WGS))

Data: how they flow; formats, pipelines, storage & maintenance 

Mapping reads & calling variants; thresholds; from SNVs to SVs 

Practical Sessions UNIX basics and Genomic pipeline for SNV

and indel Quality metrics in VCF and BAM files (FORMAT & IGV) 

Practical Session Standards (HGVS and HPO) and sharing data 

 

The technique and rationale when ordering a clinical test: Panels

x Exome x Genomex Focused Exome

Variant databases & the importance of sharing data DNA

diagnostics = share variants & phenotype 

Annotationand prioritization of variants with use of ACMG2015 

Genome browsers; UCSC 

Practical Session CNV calling

Practical Session UCSC usage

Organization of a center of NGS, from services to research. 

WES/WGS in practice; successes, failures, secondary findings 

Identification of novel gene-disease associations 

Functional validation of variants; RNA, protein, expression,

functional assays 

NGS Diagnostics using LOVD+

ELSI aspects; ethical, legal and social issues in Brazil 

Interesting cases in craniofacial and skeletal dysplasias in the

topic from research to diagnosis (and back) 

Future developments

Day 1

Day 3

Day 2

Day 4