Table 4

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


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

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.

Cheung et al. Genome Biology 2003 4:R25   doi:10.1186/gb-2003-4-4-r25

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