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Table 2 Variants defined as “true”

From: Copy number variations in candidate genomic regions confirm genetic heterogeneity and parental bias in Hirschsprung disease

Chromosomal region (chr:start-end)candidate regionaberrat. Type# probesreported on DGVreported on decipher (# individuals)confirmation on available replicate/sselected for validationsample(s) and variant # (N) bgenes
1:146638075–147,824,207genome (1q21)loss4NY (1q21.1 recurrent microdel)confirmedYHSCR019, #21 (1)PRKAB2, PDIA3P, FMO5, CHD1L, BCL9, ACP6, GJA5, GJA8, GPR89B, GPR89C, PDZK1P1, LOC200030, NBPF11
4:41746863–41,751,291PHOX2Bloss11NNconfirmedYHSCR403, #69 (1)PHOX2B
5:69288477–70,309,855genome (5q13)gain3Y (freq ≥5%)Nnot excludedNHSCR016, #18 (1)SERF1A, SMN2, NAIP, SMA4, GTF2H2B, LOC441081, DQ591060
7:84217007–84,225,649SEMA3A/ SEMA3Dloss4Y (freq < 1%)NYHSCR005, #5 (1)(SEMA3A; SEMA3D)(SEMA3A; SEMA3D)
8:32597644–32,598,929NRG1loss3NNYHSCR045, #29 (1)NRG1
9:109273643–109,275,6949q31loss2NNYHSCR043, #27 (1)(TMEM38B; ZNF462)(TMEM38B; ZNF462)
9:109336464–109,348,4679q31gain6NNYHSCR018, #20 (1)(TMEM38B; ZNF462)(TMEM38B; ZNF462)
9:110381888–110,401,9999q31gain9NNconfirmedYHSCR000, #1 (1)(KLF4; ACTL7B)(KLF4; ACTL7B)
9:112078131–112,089,1939q31loss5NNconfirmedYHSCR195, #42 (1)EPB41L4B
9:113025039–113,029,4309q31loss2Y (freq ≥5%)Y (1)NHSCR415, #77 (1)(TXN; TXNDC8)(TXN; TXNDC8)
9:43659247–43,659,512genome (9p11)loss (3) / gain (1)2Y (freq ≥5%)NconfirmedNHSCR162, #38; HSCR403, #70; HSCR421, #78; HSCR426, #80 (4)(SPATA31A6; CNTNAP3B)(SPATA31A6; CNTNAP3B)
15:20848460–22,432,687genome (15q11)loss (4) / gain (6)5Y (freq ≥5%)Nnot excludedNHSCR010, #13; HSCR033, #22; HSCR064, #33; HSCR160, #181; HSCR181, #39; HSCR231, #45; HSCR335, #54; HSCR382, #67; HSCR409, #74; HSCR414, #76 (10)NBEAP1, POTEB, CXADRP2, OR4M2, OR4N4, OR4N3P
15:58257674–59,009,890genome (15q21)gain2NNYHSCR146, #35 (1)ALDH1A2, AQP9, LIPC, ADAM10, HSP90AB4P
16:82200334–82,202,46716q23.3gain2NNYHSCR217, #43 (1)MPHOSPH6
19:31954093–31,966,03619q12loss5NNnot evaluableYHSCR481, #82 (1)(TSHZ3; THEG5)(TSHZ3; THEG5)
22:18661724–18,920,00122q11.2gain7Y (freq ≥5%)Nnot evaluableNHSCR58, #32 (1)AK302545, BC112340, DGCR6, PRODH
22:20345868–20,499,78922q11.2gain4Y (freq ≥5%)Nnot excludedNHSCR335, #56 (1)TMEM191B, RIMBP3
22:21494163–21,704,972a22q11.2gain5NNconfirmedNHSCR403, #72 (1)cGGT2, POM121L7
22:22417683–23,228,48322q11.2loss15Y (freq ≥5%)NNHSCR014, #17 (1)VPREB1, ZNF280B, ZNF280A, PRAME, LOC648691, GGTLC2
22:22781091–23,228,48322q11.2loss8Y (freq ≥5%)NNHSCR036, #23; HSCR183, #41 (2)ZNF280B, ZNF280A, PRAME, LOC648691, GGTLC2
22:23056562–23,228,48322q11.2loss3Y (freq ≥5%)NconfirmedNHSCR403, #73 (1)(GGTLC2; IGLL5)
22:25672585–25,892,40122q11.2loss (1) / gain (2)5Y (freq ≥5%)Y (3)not excludedNHSCR016, #19; HSCR228, #44; HSCR421, #79 (3)LRP5L, CRYBB2P1
  1. Variants have been defined as “true” when either reported on DGV, confirmed on a second array replicate, or validated with a different approach (see follow up in Table 4)
  2. Genes between brackets are those flanking the CNV when no gene is affected by the aberration
  3. not selected for validation because initially considered unlikely at the visual inspection
  4. b the code for the sample in which the CNVs has been detected is reported, together with the variant call # as indicated in the Additional file 1 and, among brackets, the number of times the CNVs has been detected in the 59 samples
  5. c this CNV was detected also in other two samples, for which neither replication nor validation through a different approach were carried out. For this reason, these are not included in the count of the true variants