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MOLECULAR GENETICS:

HOW IT HELPS THE CLINICIAN

Don Love

Diagnostic Genetics

SINGLE GENE

MULTIPLE GENES

VARIANT CALLS AND

CLASSIFICATIONS

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SINGLE GENE

MULTIPLE GENES

VARIANT CALLS AND

CLASSIFICATIONS

Taken from: Waheed, Mol Vis 2012; 18:1253-1259. http://www.molvis.org/molvis/v18/a131

GENE STRUCTURE

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SINGLE GENE

MULTIPLE GENES

VARIANT CALLS AND

CLASSIFICATIONS

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MASSIVELY PARALLEL SEQUENCING STRATEGIES

MASSIVELY PARALLEL SEQUENCING

(MPS)

Software Box Capture

Multiplicom

Life Technologies

Illumina

Customer-designed

Raindance RDT1000 Softgenetics

GeneSifter

Company-directed

Ion Reporter

BaseSpace

Roche AVA

GS-Junior

Ion Torrent/Proton

MiSeq/HiSeq

Fluidigm Access Array

Real Time Genomics

SeqPilot

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LQTS

KCNQ1

KCNH2

SCN5A

KCNE1

KCNE2

KCNJ2

CACNA1C

SQTS

KCNH2

KCNQ1

CACNA1C

CACNB2

BrS

SCN5A

CACNA1C

CACNB2

SCN1B

SCN10A

CPVT

RYR2

CASQ2

HCM

MYH7

MYBPC3

TNNT2

TPM1

TNNI3

MYL2

MYH6

GLA

DCM

TTN

MYH7

LMNA

SCN5A

TNNI3

TNNT2

MYBPC3

BAG3

ARVC

PKP2

DSG2

DSP

RYR2

DSC2

MPS APPROACH FOR A CARDIAC GENE PANEL

Agilent Sure Select Capture Illumina MiSeq JSI SeqNext software

MULTIPLE GENES

MULTIPLE PATIENTS

CARDIAC GENE PANELS

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Whole genome

Whole exome

Clinical-based

exome

Custom gene

panels

SINGLE GENE

MULTIPLE GENES

VARIANT CALLS AND

CLASSIFICATIONS

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DATA ANALYSIS

Read Depth

Coverage Diagnostics/Screening

ACMG CRITERIA

Genet Med. 2015 May;17(5):405-24.

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LSDB: Locus-specific database *In a gene where loss of function is a known mechanism of disease

LSDB: Locus-specific database *In a gene where loss of function is a known mechanism of disease

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NM_000238.3(KCNH2):c.[3224C>T];[=]

NP_000229.1(KCNH2):p.[(Pro1075Leu)];[=]

The missense variant, c.3224C>T p.(Pro1075Leu), in the KCNH2 gene, is classified as of uncertain significance (Class 3) based on the following evidence:

* It is only present at very low frequency in general population databases [1-3].

* It is listed as probably pathogenic in the LOVD LQTS database [4], but it is only referred to in the literature as being identified in this patient [5].

* In-silico bioinformatic predictions are conflicting for this variant [6-9].

References:

[1] 1000Genomes: http://www.1000genomes.org; [2] ExAC: http://exac.broadinstitute.org/; [3] ESP: http://evs.gs.washington.edu/EVS; [4] LOVD LQTS Database: www.genomed.org/lovd2; [5] Chung S et al., Heart Rhythm 2007;4(10):1306-1314.; [6] PolyPhen-2: http://genetics.bwh.harvard.edu/pph2/; [7] SIFT: http://sift.bii.a-star.edu.sg/www/SIFT_BLink_submit.html; [8] SNPs&GO: http://snps-and-go.biocomp.unibo.it/snps-and-go/; [9] PROVEAN: http://provean.jcvi.org/protein_batch_submit.php?species=human

REPORTING A CLASS 3 VARIANT

SOME TIMES CLARITY PROVES ELUSIVE

Einstein discovers that time is actually money

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