Genome-wide characterization of copy number variants in epilepsy - PowerPoint PPT Presentation

Genome-wide characterization of copy number variants in epilepsy patients Canadian Human and Statistical Genetics Meeting Jean Monlong April 24, 2017 B OURQUE L AB M C G ILL U NIVERSITY H UMAN G ENETICS D EPT .

Copy Number Variation (CNV) Imbalanced genetic variation involving more than 500bp. 2

Epilepsy Neurological disorder characterized by recurrent and unprovoked seizures. Incidence 3%. Rare large CNVs were associated with epilepsy (array-based studies). The Canadian Epilepsy Network (CENet) conducted whole-genome sequencing of epilepsy patients to identify genetic variants that predispose individual to epilepsy or drug response. 3

Detecting CNV in Whole-Genome Sequencing Read coverage variation 4

Detecting CNV in Whole-Genome Sequencing Read coverage variation PopSV: Population-based approach Use a set of reference experiments to detect abnormal patterns. number of reads mapped sample reference tested genomic window 4

PopSV’s workflow 5

PopSV is more sensitive than other methods Twin dataset, normal/tumor cancer dataset and RT-PCR validation. PopSV FREEC ● cn.MOPS CNVnator LUMPY ● 100 200 300 number of replicated calls per sample PopSV FREEC cn.MOPS ● CNVnator LUMPY ● 0.00 0.25 0.50 0.75 1.00 proportion of replicated calls per sample 6

Application to the CENet dataset 7

Application to the CENet dataset Frequency from 5 public WGS-derived SV databases. Rare means frequency < 1% in all 5 databases. 8000 rare 6000 common CNV 4000 2000 0 0 0.01 0.1 0.25 0.5 1 maximum frequency in the public databases 7

Slight enrichment of rare CNVs in exons all CNVs rare CNVs ● 1.0 ● ● ● ● ● fold−enrichment ● 0.8 controls ** ● ** patients ** 0.6 ● ● ● ● all genes LoF all genes LoF intolerant intolerant genes genes fold-enrichment: how many CNVs overlap an exon compared to expected by chance. Loss-of-Function intolerant genes from ExAC consortium. 8

Rare exonic CNVs are more recurrent in the epilepsy cohort ● proportion of rare exonic CNVs 0.075 ● 0.050 controls ● ● patients ● 0.025 ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● 0.000 2+ 3+ 4+ 5+ 6+ 7+ 8+ 9+ 10+ CNV recurrence 9

Putatively pathogenic exonic CNVs 10

Putatively pathogenic exonic CNVs 8/21 affect a known epilepsy-associated gene (Ran NAR 2015) . 93.3 mb 93.5 mb 93.4 mb Gene CHD2 CNV CNET0119 CNET0130 CNET0143 2000 Coverage ● ● ● ● ● ● ● ● ● 1500 ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● 1000 CNET0119 CNET0130 CNET0143 Two recurrent CNVs were replicated in an additional cohort (325 patients and 380 controls). 10

Rare non-coding CNVs enriched close to epilepsy-associated genes 150 cumulative affected samples 100 controls patients 50 0 0 100 200 300 distance to nearest epilepsy exon (kb) 11

Even more if in enhancers of the epilepsy gene 80 60 cumulative affected samples controls 40 patients 20 0 0 100 200 300 distance to nearest epilepsy exon (kb) Enhancer: eQTL or DNase site associated with the epilepsy gene. 12

Conclusions Rare exonic CNVs are enriched and more recurrent in epilepsy patients compared to controls. Identified putatively pathogenic exonic CNVs , some replicated in an additional cohort. Rare non-coding CNVs are enriched close to epilepsy-associated genes. We show the importance of small and non-coding CNVs in epilepsy. Comprehensive profiling of CNVs could help explain a larger fraction of epilepsy cases . 13

Acknowledgment Poster 8 Guillaume Bourque Simon L. Girard Patrick Cossette Pascale Marquis Caroline Meloche Guy Rouleau Mathieu Bourgey Maxime Cadieux-Dion Dan Spiegelman Louis Letourneau Micheline Gravel Alexandre Francois Lefebvre Ron G. Lafreniere Dionne-Laporte Eric Audemard Michel Boivin Toby Hocking Jacques L. Michaud Danielle M. Andrade Patricia Goerner-Potvin Fadi Hamdan Cyrus Boelman Simon Gravel Berge A. Minassian Mathieu Blanchette 14

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Technical bias in WGS shuffled shuffled simulated simulated WGS WGS 1200 1300 1400 1500 1600 1700 100 200 bin inter−sample mean coverage bin inter−sample standard deviation 16

Technical bias in WGS coverage ● highest ● 0.05 lowest propotion of the studied genome ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● 0.00 ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● −0.05 ● −0.10 sample 17

Twin pedigree concordance 1.00 method LUMPY ● Rand index using pedigree information CNVnator ● cn.MOPS ● ● FREEC ● ● 0.75 PopSV ● ● ● ● clustering linkage ● ● average ● complete ● ● Ward 0.50 ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● 0.25 ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● 0.00 ● ● ● ● ● ● ● ● ● ● 0 10 20 30 40 number of groups derived from CNV clustering 18

RT-PCR validation rates Region Validation rate Total 151 0.907 CNV type Deletion 102 0.902 Duplication 49 0.918 Frequency in database 0 26 0.923 (0 , 0 . 01] 24 0.833 (0 . 01 , 1] 101 0.921 Size (Kbp) < 20 73 0.849 (20 , 100] 38 0.974 > 100 40 0.950 19

Size distribution 600 WGS 400 average number of CNV per sample 200 0 30 20 array 10 0 <10 10−50 50−100 100−200 200−500 >500 CNV size (Kbp) 20

Large CNV enrichment in epilepsy patients all CNVs rare CNVs 1.0 ● ● ● ● 0.8 fold−enrichment ● ● ● controls 0.6 patients 0.4 all genes LoF all genes LoF intolerant intolerant genes genes 21

Non-coding CNVs of high interest 22

Rare deletions enriched in epilepsy-associated genes ● ● ● 1.5 ● ● ● ● ● ● ● ● ● ● deletion 1.0 ● ● ● ● ● 0.5 ● controls fold−enrichment ● patients 0.0 twins ● P−value ● 1.5 <0.05 ● >0.05 ● ● ● ● ● ● duplication 1.0 ● ● ● ● ● ● ● ● ● ● ● ● 0.5 0.0 0 1e−04 0.001 0.01 0.1 1 CNV frequency in public databases 23

Rare deletions enriched in epilepsy-associated genes Genes hit deletions never seen in public databases 1500 observed number of sampling 1000 500 0 0 5 10 15 20 number of epilepsy genes among sampled genes sampling all genes size−controlled genes 24