SINGLE GENE MULTIPLE GENES VARIANT CALLS AND … 1330 Donald Love CSNZ_290617.pdf · 2017. 11....
Transcript of SINGLE GENE MULTIPLE GENES VARIANT CALLS AND … 1330 Donald Love CSNZ_290617.pdf · 2017. 11....
21/07/2017
1
MOLECULAR GENETICS:
HOW IT HELPS THE CLINICIAN
Don Love
Diagnostic Genetics
SINGLE GENE
MULTIPLE GENES
VARIANT CALLS AND
CLASSIFICATIONS
21/07/2017
2
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
21/07/2017
3
SINGLE GENE
MULTIPLE GENES
VARIANT CALLS AND
CLASSIFICATIONS
21/07/2017
4
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
21/07/2017
5
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
21/07/2017
6
Whole genome
Whole exome
Clinical-based
exome
Custom gene
panels
SINGLE GENE
MULTIPLE GENES
VARIANT CALLS AND
CLASSIFICATIONS
21/07/2017
7
DATA ANALYSIS
Read Depth
Coverage Diagnostics/Screening
ACMG CRITERIA
Genet Med. 2015 May;17(5):405-24.
21/07/2017
8
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
21/07/2017
9
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
https://www.google.co.nz/search?hl=en&site=imghp&tbm=isch&source=hp&biw=1334&bih=682&q=are+you+helping&oq=are+you+helping&gs_l=img.3..0i24k1.2232.10599.0.11435.21.18.
2.0.0.0.232.2864.0j6j8.14.0....0...1.1.64.img..5.15.2646...0j0i10i24k1.DDZrDQcBqok#hl=en&tbm=isch&q=helping,+larson++cartoon&imgrc=hlcRUWuGSTS0tM: