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Table 4 Concordance of ClinSV with pathogenic variants from aCGH. Comparison of pathogenic CNVs identified by aCGH and WGS using ClinSV on matched DNA from the same patients. Eleven patients with known pathogenic variants were compared. Genomic coordinates are listed compared to the GRCh37 reference genome build. Sample A4 had a large CNV identified by aCGH, which was disrupted by a 7.3-kb diploid region in the middle

From: ClinSV: clinical grade structural and copy number variant detection from whole genome sequencing data

Sample

aCGH calls

WGS calls

A1

22q11.21 (18,894,835–21,505,417) × 1

del(22)(q11.21q11.21) chr22:g.18,873,701_21,466,500del

A2

22q11.21 (18,894,835–21,505,417) × 3

dup(22)(q11.21q11.21) chr22:g.19,025,201_21,502,400dup

A3

15q11.2q13.1 (23,656,936–28,559,402) × 1

del(15)(q11.2q13.1) chr15:g.23,679,001_28,659,900del

A4

15q11.2q13.3 (22,765,628–32,418,879) × 3–4

dup(15)(q11.2q13.2) chr15:g.22,727,651_30,670,600dup, dup(15)(q13.2q13.3) chr15:g.30,677,901_32,679,700dup

A5

(X) ×1

del(X)(p22.33q28) chrX:g.pter_cen_qterdel

A6

(X) ×2,(Y) ×1

dup(X)(p22.33q28) chrX:g:pter_cen_qterdup

A7

4p16.3 (1,832,643–1,994,922) ×1

del(4)(p16.3p16.3) chr4:g.1,830,325_1,996,237del

A8

16p11.2 (29,849,168–30,190,568) ×1

del(16)(p11.2p11.2) chr16:g.29,560,701_30,200,100del

A9

Xp22.33p22.31 (60,701–8,392,011) ×1, Yq11.221q12(16,188,682–59,335,913) × 1

der(X)t(X;Y)(p22.31;q11.221) g.[chrX:pter_8,434,700delinschrY:16,097,288_qterinv]

A10

Xp21.1 (32,714,410-32,868,014) × 0

del(X)(p21.1p21.1) chrX:g.32,707,584_32,871,077del

A11

15q11.2 (22,765,628-23,077,909) × 3

dup(15)(q11.2q11.2) chr15:g.22,727,651_23,377,700dup