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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.