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Table 4 Cases with inconsistent results between NGS and SNP array, and validation by qPCR

From: Clinical outcome of preimplantation genetic diagnosis and screening using next generation sequencing

Embryo

Embryo grade

Indications of PGD/PGS

NGS results

SNP-array results

qPCR validation

P05-1

5BB

46,XX,t(1;2)(q23;q31)

seq 1q25.3 → qter(181509440–246832193)×3

No aberration of 1

1(q25.3-qter) gain

   

seq 2q31.3 → qter(182458386–242690112)×1

arr 2q32 → qter(180777009–242650581) ×1

 

P06-1

5BB

AMA, RM

seq 2q22.1 → qter(137671536–238692973)×3

arr 2q23.1 → q36.1(149105998–223098449)×3

   

seq 5q12.3 → q35.3(65909293–180786350)×1

arr 5q23.3 → qter(131821983–180629495)×1

 
   

seq 8q11.23 → q23.1(53409090–109384199)×3

arr 8q12 → q23(56748900–112484426)×3

 
   

No aberration of 19

arr 19q13.11 → qter(38709901–63731511)×1

19q13 normal

   

seq 20q13.12 → qter(45325082–60016946)×1

arr 20q11.21 → qter(30108048–62376958)×1

 

P06-4

5BC

AMA, RM

seq 2pter → p22.3(1–34106490)×3

arr 2pter → p23(24048–2928815)×3

 
   

seq 12pter → p12.1(16037–25938212)×1

arr 12pter → p12(50446–19567738)×1

 
   

seq 14q11.2 → q23.3(19373466–64143228)×1

No aberration of 14

14(q11.2-q23.3) loss

   

seq 16pter → qter(1606029–88555348)×3

arr 16pter → q13(31010–48646787)×3

 

P07-3

3BC

46,XX,inv(6)(p21q25)

No aberration of 2

arr 2q10 → q13(94914686–110337634)×3

2(q10-q13) normal

   

seq 19pter → qter(12244–63686007)×3

arr 19pter → qter(1–63686007)×3

 

P21-1

5BC

46,XY,t(8;18)(p11;q21)

seq 8pter → p12(384809–31731414)×1

arr 8pter → p12(180568–33542048)×1

 
   

seq 18q22.1 → qter(62606544–75622883)×3

arr 18q22.3 → qter(6906594–76115554)×3

 
   

seq Ypter → qter(2784907–27141653)×2

No aberration of Y

Y chromosome gain

P23-5

3BC

46,XX,t(1;8)(q32;q22)

seq 4pter → p12(4–48354873)×3

No aberration of 4

4p gain

   

seq 8q21.3 → q24.22(92180303–135064173)×1

arr 8q21.1-qter(113497800–146263569)×1

 
   

seq 12pter → qter(251302–132143742)×1

arr 12pter → qter(50446–132287718)×1

 
   

seq 15pter → qter(776958–99963983)×3

arr 15pter → qter(18427103–100192115)×3

 
   

seq 17pter → qter(444930–77158450)×1

arr 17pter → qter(18901–78599918)×1

 

P24-1

5BB

46,X,inv(X)(p11q22)

seq 3pter → qter(1–199501827)×3

arr 3pter → qter(1–199501827)×3

 
   

seq 4pter → p15.1(3–35468007)×3

No aberration of 4

4(pter-p15.1) gain

   

seq 16pter → qter(1749–88827254)×3

arr 16pter → qter(1–88827254)×3

 
  1. PGD: preimplantation genetic diagnosis; PGS: preimplantation genetic screening; NGS: next generation sequencing; SNP: single nucleotide polymorphism; qPCR: quantitative polymerase chain reaction.