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Table 1 Characteristics of structural rearrangements involving palindrome P8

From: Birth, expansion, and death of VCY-containing palindromes on the human Y chromosome

Cell line

VCY CN

Hg

Rearrangement summary

Novel junction structure

Data types

Similar samples

Possible mechanisms

HG00742

1

R1b-L11

37.8-kb deletion removing one P8 arm

14-bp insertion

Fiber-FISH 10x

 

NHEJ

HG01781

3

J2a-M410

31.5-kb inverted duplication expanding P8 to 113.8 kb

Recombination within 92-bp duplicated region

Fiber-FISH 10x

HG01991

NAHR or BIR

HG02390

3

O2-K18

191.3-kb tandem duplication distal to P8

Recombination within 2-bp microhomology region

Fiber-FISH 10x

HG01031, HG02401, HG00982

MMBIR

HG01377

4

E1b-M35

Complex formation of additional 436.7-kb new palindrome

Recombination within 5-bp microhomology region

Fiber-FISH 10x

 

MMBIR

HG01097

3

G-M201

158.1-kb tandem duplication distal to P8

Recombination within 6-bp microhomology region

Fiber-FISH 10x

 

MMBIR

HG04131

3

R1a-Z93

70.1-kb tandem duplication distal to P8

Complex recombination within 5.1-kb duplicated region

Fiber-FISH 10x

 

NAHR or BIR

NA18953

3

O2b-M176

60.5-kb tandem duplication proximal to P8

Recombination within 5.1-kb duplicated region

Fiber-FISH 10x

 

NAHR or BIR

HG00707*

3

O3-M122

60.5-kb tandem duplication proximal to P8

Fiber-FISH

 

  1. Abbreviations: CN copy number, Hg haplogroup (haplogroup defined from previous work [16]), NHEJ non-homologous end joining, NAHR non-allelic homologous recombination, BIR break-induced replication, MMBIR microhomology-mediated break-induced replication
  2. *HG00707 showed a similar fiber-FISH structure to NA18953 but was not sequenced using 10x Genomics Linked-Read sequencing