Detailed analysis of 15q11-q14 sequence corrects errors and gaps in the public access sequence to fully reveal large segmental duplications at breakpoints for Prader-Willi, Angelman, and inv dup(15) syndromes - PubMed (original) (raw)

Detailed analysis of 15q11-q14 sequence corrects errors and gaps in the public access sequence to fully reveal large segmental duplications at breakpoints for Prader-Willi, Angelman, and inv dup(15) syndromes

Andrew J Makoff et al. Genome Biol. 2007.

Abstract

Background: Chromosome 15 contains many segmental duplications, including some at 15q11-q13 that appear to be responsible for the deletions that cause Prader-Willi and Angelman syndromes and for other genomic disorders. The current version of the human genome sequence is incomplete, with seven gaps in the proximal region of 15q, some of which are flanked by duplicated sequence. We have investigated this region by conducting a detailed examination of the sequenced genomic clones in the public database, focusing on clones from the RP11 library that originates from one individual.

Results: Our analysis has revealed assembly errors, including contig NT_078094 being in the wrong orientation, and has enabled most of the gaps between contigs to be closed. We have constructed a map in which segmental duplications are no longer interrupted by gaps and which together reveals a complex region. There are two pairs of large direct repeats that are located in regions consistent with the two classes of deletions associated with Prader-Willi and Angelman syndromes. There are also large inverted repeats that account for the formation of the observed supernumerary marker chromosomes containing two copies of the proximal end of 15q and associated with autism spectrum disorders when involving duplications of maternal origin (inv dup[15] syndrome).

Conclusion: We have produced a segmental map of 15q11-q14 that reveals several large direct and inverted repeats that are incompletely and inaccurately represented on the current human genome sequence. Some of these repeats are clearly responsible for deletions and duplications in known genomic disorders, whereas some may increase susceptibility to other disorders.

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Figures

Figure 1

Figure 1

Map showing an overview of build 36 for 15q11-q14. The positions and orientations of the proximal eight contigs of 15q are shown as in build 36, with the HERC2 duplications (segments P, V, and Y) shown in detail. The asterisk above segment V of RP11-536P16 is to indicate that its orientation is shown as in the database. The positions of the seven gaps are shown with the approximate positions of the PWS/AS breakpoint (BP)1 to BP3. The map is divided into three parts for analysis in Figures 2, 3 and 5, as indicated. Mb, megabases.

Figure 2

Figure 2

Map of 15q13-q14 at proximal end of contig NT_010194. This part of the map is an updated version of the same region that we analyzed previously [20], with some differences in segment labeling. RP11 clones representing the two possible haplotypes are arbitrarily placed either above or immediately below the segments, with the non-RP11 clones placed below the contig label. Asterisks indicate representative clones used in the contig. Solid lines indicate completely sequenced clones, and dotted lines indicate draft sequences (high throughput genomic sequences [htgs]). A solid line with a dotted line extension indicates a clone in which only a part has been completely sequenced. A gap in a clone indicates a deletion. kb, kilobases.

Figure 3

Figure 3

Map of contigs NT_078095, NT_010280, and NT_078096 (15q12-q13). The clones are indicated as in Figure 2. kb, kilobases.

Figure 5

Figure 5

Map of contigs NT_037852, NT_077631, NT_078094, and part of NT_026446 (15q11-q12). The clones are indicated as in Figure 2. The shaded segment indicates α-satellite DNA sequence. Note that clones CTD-2298I13, CTC-803A3, and 386A2 occur twice to indicate two possible locations with respect to the RP11 sequence. kb, kilobases.

Figure 4

Figure 4

Alignment of 15q11-q13 clones in duplicons adjacent to segment V. (a) The three representative clones containing segment V are aligned, with single nucleotide variants in a 3,356 base pair (bp) region of segment V in all sequenced RP11 clones shown below. The asterisk above segment V indicates its orientation, as in Figure 1. The box shows the number of mismatches between each pair of haplotigs. (b) Corrected alignment of clones to show true relationship between ends of contigs NT_010280 and NT_078096. The hash above segment V of RP11-536P16 is to indicate that its orientation has been inverted compared with that in the database. (c) Alignment of clones around the segment V end of contig NT_078094, with single nucleotide variants in a 9.5 kilobase (kb) region around the small segment P shown below.

Figure 6

Figure 6

Analysis of symmetrical region near the centromeric end of 15q to identify its likeliest arrangement in RP11. The region between the most proximal segments P ordered as in Figure 5 is indicated by the four rows of segments at the top. The first row, continuing to the third row, represents the upper RP11 haplotigs in Figure 5 and the second row, continuing to the fourth row, represents the lower haplotigs. The RP11 haplotigs are shown below the segments with the non-RP11 clones shown further below. Nine slices of 5 to 30 kilobases (kb), shown by alternating red or blue lines, were investigated, with each box showing the number of single nucleotide mismatches between each pair of RP11 haplotigs and non-RP11 clones in the slice.

Figure 7

Figure 7

Map showing positions of segmental duplications of 15q11-14 in the RP11 individual. The main part of the map shows the segmental duplications as in Figures 2, 3 and 5, with the approximate positions of genes, duplications (dup), and pseudogenes (ps) shown underneath and the positions of the three remaining contigs at the bottom. Note that most of the imprinted region in the Prader-Willi/Angelman syndrome critical region is not included. The alternative structure (model B) near the centromere is shown underneath. The duplicated regions in each of the five breakpoint regions (BP1 to BP5) are shown in more detail above the map and include the probable structure for those individuals with a BP2:BP3 inversion. The positions of the major direct and inverted repeats are shown above the detail with arrows in an arbitrary direction.

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References

    1. Knoll JH, Nicholls RD, Magenis RE, Graham JM, Jr, Lalande M, Latt SA. Angelman and Prader-Willi syndromes share a common chromosome 15 deletion but differ in parental origin of the deletion. Am J Med Genet. 1989;32:285–290. doi: 10.1002/ajmg.1320320235. - DOI - PubMed
    1. Christian SL, Robinson WP, Huang B, Mutirangura A, Line MR, Nakao M, Surti U, Chakravarti A, Ledbetter DH. Molecular characterization of two proximal deletion breakpoint regions in both Prader-Willi and Angelman syndrome patients. Am J Hum Genet. 1995;57:40–48. - PMC - PubMed
    1. Wandstrat AE, Schwartz S. Isolation and molecular analysis of inv dup(15) and construction of a physical map of a common breakpoint in order to elucidate their mechanism of formation. Chromosoma. 2000;109:498–505. - PubMed
    1. Buckton KE, Spowart G, Newton MS, Evans HJ. Forty four probands with an additional 'marker' chromosome. Hum Genet. 1985;69:353–370. doi: 10.1007/BF00291656. - DOI - PubMed
    1. Crolla JA, Harvey JF, Sitch FL, Dennis NR. Supernumerary marker 15 chromosomes: a clinical, molecular and FISH approach to diagnosis and prognosis. Hum Genet. 1995;95:161–170. doi: 10.1007/BF00209395. - DOI - PubMed

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