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Table 4 Segmental duplications involved in known genomic disorders and chromosome rearrangements identified by BLAST and ambSNP analyses

From: Genome-wide detection of segmental duplications and potential assembly errors in the human genome sequence

  

First copy

Second copy(s)

  

Disorders

Band

Start*

Size*

ambSNPs†

Start*

Size*

ambSNPs†

Identity

Celera C4 ‡

Gaucher disease

1q22

148108965

10,649

7

152776301

-10,479

10

95.19

S

Spinal muscular atrophy

5p14/5q13

21621854

79,183

1,032

69175603

-79,149

1,190

98.22

M

Williams-Beuren syndrome

7q11.23

70970126

359,416

380

72927299

111,773

56

99.60

P

     

73383317

-227,260

355

99.20

P

t(4;8)(p16;p23) Wolf-Hirschhorn syndrome

4p16/8p23

8769778

99,609

3†

7156209

-51,677

18

95.65

P

     

7470072

-82,189

387

95.81

P

inv dup(8p) der(8)(8p23.1::p23.2-pter) del(8)(p23.1p23.2)

8p23.1

7084847

138,560

123

7756853

-126,769

229

99.16

M

     

7651975

54,807

463

96.93

M

Prader-Willi syndrome and Angelman syndrome

15q11/15q13

19709020

75,325

102

19961243

34,902

55

98.70

P

     

20029574

41,965

83

98.79

P

  

19802418

251,245

548

20064937

74,780

65

99.01

P

Polycystic kidney disease 1

16p13

2164789

38,034

136

16249164

24,076

243

98.32

P

Charcot-Marie-Tooth1A/Hereditary neuropathy with pressure palsies

17p12/17p12

14440158

23,599

272

15837032

23,585

286

98.42

P

Smith-Magenis syndrome/ dup(17)(p11.2-p11.2)

17p12

18524425

152,700

547

20492073

-147,255

539

99.06

M

     

25811482

28,239

24

99.20

M

Neurofibromatosis type 1

17q11.2

28686414

63,356

163

28952984

-32,619

129

98.65

P

DiGeorge syndrome and velocardiofacial syndrome

22q11.21

15662253

155,811

471

18221385

155,996

322

99.42

P

     

17742343

9,740

62

97.84

P

     

18164371

-39,696

21

99.37

P

Chronic myeloid leukemia t(9;22)(pq34;q11)

9q34/ 22q11

123263651

36,956

NA

20552124

26,424

NA

91.81

S

Emery-Dreifuss muscular dystrophy

Xq28

147627873

11,030

2

147676529

11,034

2

99.61

S

Shwachman-Diamond syndrome

7q11.21

65091051

325,140

665

70647188

302,881

652

97.43

P

Red green color blindness

Xq28

148439480

21,144

61

148476598

21,834

58

99.82

S

BRCA1 duplication

17q21

40983970

43,221

66

62252214

431,52

66

99.85

P

Male infertility AZFc microdeletion region 2

Yq11.22

23322362

190,336

391§

23680552

-185,149

393§

99.88

P

 

Yq11.22

23908727

94,194

282§

24794944

-93,690

284§

99.92

P

 

Yq11.22

24794944

93,690

247§

27460935

-94,218

248§

99.93

P

  1. This table represents a partial list of all known genomic disorders and chromosome rearrangements. *Only the start coordinates (based on June 2002 assembly) for duplicons are shown. Results from BLAST analysis with chromosome coordinates and size of duplicon. For several genomic mutations (Williams-Beuren syndrome, Prader-Willi syndrome and Angelman syndromes, and DiGeorge syndrome) the duplicons shown are incomplete, most of which are composed of several duplication modules. The '-' sign indicates that the second duplicon is in the inverse orientation. †The number of ambSNPs (ambiguously mapped single-nucleotide polymorphisms) found within the genomic segment. NA, not applicable. The ambSNP analysis defines regions containing high densities of contiguous ambSNPs. For some of the segmental duplications involved in genomic disorders, the contiguous lengths of ambSNPs are much larger than those detected by BLAST. The specific sizes of the segmental duplications have to be resolved by detailed characterization of the different modules. ‡Celera representation: S, both copies found in large (> 500 kb) sequence scaffolds; P, partially hit, single copy found, or less than perfect alignments; M, missing from large sequence scaffolds, hitting numerous fragments. § SNPs with multiple locations were used for evaluating the density of ambSNPs.
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Genome Biology

ISSN: 1474-760X

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