Identification of two highly polymorphic CA-repeats (D21S1224 and D21S1261) on human chromosome 21q22.3

Two highly polymorphic CA-repeat microsatellites (D21S1224 and D21S1261) are reported. The clones containing these CA-repeats (ABM-C60 and ABM-C29) have been isolated from a human chromosome-21-specific library (LA21NS01) and have been localised to the q22.3 band using a specific chromosome 21 somatic cell hybrid panel. Both polymorphisms showed heterozygosities of 0.83 in the unrelated reference parents from the Centre d'Etude du Polymorphisme Humain. These new markers should improve the map of the 21q22.3 region, which is believed to contain a large number of genes.     

A Contiguous Physical Map of the Pericentromeric Region of Chromosome 21q between D21Z1 and D21S13E

We constructed a long range restriction map of the pericentromeric 21q region between the centromere, identified by the alphoid DNA sequence D21Z1, and D21S13E. The physical map showed the order and intermarker distances of five new loci, including two for which highly informative dinucleotide repeat polymorphisms were identified. The total distance between D21Z1 and D21S13E was 2400 kb. Comparison of genetic and physical distances indicated that there is about 400 to 500 kb per centimorgan that is not significantly different from the average 470 kb per centimorgan for the whole of chromosome 21q. Our physical mapping results do not indicate suppression of recombination in pericentromeric 21q.     

Linkage mapping of the highly informative DNA marker D21S156 to human chromosome 21 using a polymorphic GT dinucleotide repeat

A (GT)n repeat within the anonymous DNA sequence D21S156 was shown to be highly polymorphic in DNA from members of the 40 CEPH families. At least 12 alleles of this locus were recognized by electrophoresis on polyacrylamide gels of DNA amplified by the polymerase chain reaction (PCR) using primers flanking the (GT)n repeat. The polymorphism information content was 0.82. PCR amplification of DNA from somatic cell hybrid lines mapped D21S156 to human chromosome 21 and linkage analysis localized this marker close to the loci ETS2, D21S3, and HMG14 on chromosomal band 21q22.3. This polymorphism is highly informative and can serve as an anchor locus for human chromosome 21.     

Subregional localization of the chromosome 21 loci D21S24 and D21S26 using physical mapping techniques

Summary We were able to refine the chromosomal position of two existing marker loci, using an extended chromosome 21 somatic cell hybrid panel. The locus D21S26 mapped in the region 21q11.2–q21.1, and the locus D21S24 in 21q22.1–q22.2. Physical and genetic analysis indicated that D21S26 is tightly linked to D21S13 and D21S16, two markers previously linked to familial Alzheimer's disease.     

Genetic variation of three autosomal STR Loci D21S1435, D21S1411, and D21S1412 in Korean population

The autosomal tetranucleotide short tandem repeat loci D21S1435, D21S1411 and D21S1412 were analyzed in samples of unrelated 200 Korean individuals. The loci showed no significant deviations from Hardy–Weinberg equilibrium. Alleles were assigned according to the International Society for Forensic Haemogenetics (ISFH) recommendations. The power of discrimination of the analyzed markers was found to be high for the populations, thereby facilitating the validation and efficiency of these STR markers in forensic human identification and paternity testing. To our knowledge, this is the first report of the nomenclature and the allele frequency data for these three STR loci in Korean population.     

Characterisation of three microsatellite polymorphisms (D21S1262, D21S1419 and D21S1421) from band 21q22.1

We have isolated three clones, containing highly polymorphic CA-repeat sequences, from a human chromosome 21 phage library (LA21NS01). These clones have been localised to band q22.1 by using a chromosome 21 somatic cell hybrid panel. D21S1262 is located between breakpoints 6918-8a1 and 32S, and D21S1419 and D21S1421 are localised between breakpoints JC6-A and MRC2G. Their observed heterozygosities range between 0.75 and 0.85 as shown by unrelated reference parents from the Centre d'Etude du Polymorphisme Humain. These highly polymorphic markers should be useful for improving the analysis of this region of chromosome 21, which contains important genes such as SOD1, GART and IFNAR.     

Linkage mapping of D21S171 to the distal long arm of human chromosome 21 using a polymorphic (AC)n dinucleotide repeat

Summary An (AC)_n repeat within the anonymous DNA sequence D21S171 was shown to be highly polymorphic in members of the 40 Centre d'Etude du Polymorphisme Humain (CEPH) families. Ten different alleles at this marker locus were detected by electrophoresis on polyacrylamide gels of DNA amplified by the polymerase chain reaction (PCR) using primers flanking the (AC)_n repeat. The observed heterozygosity was 66%. PCR amplification of DNA from somatic cell hybrids mapped D21S171 to human chromosome 21, and linkage analysis localized this marker close to the loci CD18, PFKL, D21S113 and D21S112 in chromosomal band 21q22.3. In CEPH family 12 a de novo allele has been observed in a maternally derived chromosome.     

DNA sequences surrounding the centromere of chromosome 21.

The mapping and sequencing of two clones that surround the centromere of chromosome 21 are presented. These clones specify the most proximal known low-order repeat on 21p (p21-7D) and the most proximal known single-copy sequence on 21q (pUT-B37 at locus D21S120).     

The pericentromeric 21 DNA marker pGSM21 (D21S13) contains an expressed HTF island.

The DNA marker locus D21S13, localized in the 21q11.1-q21 region, has been closely linked to familial Alzheimer's disease. We constructed a physical map of 1.7 Mb around D21S13 using probes pGSM21 and pGSE9. The results indicated that pGSM21 contains recognition sites for at least three rare-cutting restriction enzymes. The clustering of rare-cutting restriction sites is indicative of the presence of an HTF (HpaII tiny fragment) island. Restriction site mapping and methylation analysis proved that pGSM21 contains a methylation-free HTF island. Furthermore, a cDNA correlate has been isolated confirming that pGSM21 is part of an expressed sequence. Today, the gene associated with pGSM21 is the gene closest to the centromere on the 21q arm.     

Regional mapping of short tandem repeats on humanchromosome 10: Cytochrome P450 gene CYP2E, D10S196, D10S220, and D10S225

Human CYP2E encodes an ethanol-inducible cytochrome P450 monooxygenase that metabolizes various carcinogens and may therefore play a role in cancer susceptibility. An intronic (GGAT)_n · (CCTA)_n repeat element was found to display limited polymorphism in Caucasoids and was used as a sequence-tagged site for genomic amplification from somatic cell hybrids to localize CYP2E to 10q24.3-qter; using the same panel, three microsatellite markers, D10S196, D10S220, and D10S225, were mapped to 10q21. The close synteny of CYP2E, CYP2C, and CYP17 belonging to two different cytochrome P450 families suggests a central role for the long arm of chromosome 10 in the evolution of this large gene superfamily.     

Localization of the hemochromatosis gene close to D6S105.

The hemochromatosis (HC) gene is known to be linked to HLA-A (6p21.3); however, its precise location has been difficult to determine because of a lack of additional highly polymorphic markers for this region. The recent identification of short tandem repeat sequences (microsatellites) has now provided this area with a number of markers with similar polymorphic index to the HLA serological polymorphisms. Using four microsatellites--D6S105, D6S109, D6S89, and F13A--together with the HLA class I loci HLA-A and HLA-B in 13 large pedigrees clearly segregating for HC, we have been able to refine the location of the HC gene. We identified no recombination between HC and HLA-A or D6S105, and two-point analyses placed the HC gene within one centimorgan (cM) of HLA-A and D6S105 (HLA-A maximum of the lod score [Zmax] of 9.90 at recombination fraction [theta] of 0.0, and D6S105 Zmax of 8.26 at theta of 0.0). The markers HLA-B, D6S109, D6S89, and F13A were separated from the HC locus by recombination, defining the centromeric and telomeric limits for the HC gene as HLA-B and D6S109, respectively. A multipoint map constructed using HLA-B, HLA-A, and D6S109 indicates that the HC gene is located in a region less than 1 cM proximal to HLA-A and less than 1 cM telomeric of HLA-A. These pedigree data indicate an association between HC and specific alleles at HLA-A and D6S105 (i.e., HLA-A3 and D6S105 allele 8).(ABSTRACT TRUNCATED AT 250 WORDS)     

Highly polymorphic sequence at D21S1448 mapping close to D21S55, within the Down syndrome critical region

We have isolated a highly polymorphic sequence from the Down syndrome critical region on human chromosome 21. This is a particularly useful marker because it lies adjacent to the locus D21S55, which is most closely associated with the major defects on Down syndrome. Other than this marker, few other variable sequences are known in this region (including other restriction fragment length polymorphisms or CA repeats) and therefore D21S1448 will be extremely helpful not only for people studying the inheritance of portions of chromosome 21 with respect to Down syndrome, but also for those carrying out linkage analysis of the chromosome.     

Nucleotide Sequence Surrounding the Locus Marker D21S246 on Human Chromosome 21

Most ofthe human Not I linking clones identified to date areconsidered to be derived from CpG islands because ofthe recognitionsequence of this enzyme, and CpG islands have been reportedto be located around the 5' regions of genes. As a pilot study,we determined the complete nucleotide sequence (41,924 bp) ofa human cosmid clone (LL21NC02Q7A10) containing the marker D21S246originating from a Not I linking clone. As a result of sequenceanalysis, we successfully mapped and revealed the genomic genestructure for KIAA0002 previously reported as a cDNA clone.This gene consists of 15 exons and was shown to exist at theD21S246 locus on human chromosome 21q21.3–q22.1. Theseresults demonstrated that genomic marker-anchored DNA sequencingis a useful approach for the human genome project.     

D21S215 is a (GT)n polymorphic marker close to centromeric alphoid sequences on chromosome 21.

A plasmid, AWZ1, that contained a dinucleotide (GT)n repeat was identified from a chromosome 21-specific genomic library. When amplified by PCR from human genomic DNA, the repeat length was highly polymorphic between individuals; its location, D21S215, was mapped in the CEPH pedigrees by linkage analysis to the pericentromeric region of chromosome 21. It is the closest polymorphic marker to alphoid sequences on this chromosome.     

用改进的MVR-PCR方法检测河北地区汉族人群D7S21基因座多态性

为研究D7S21基因座在河北汉族人群分布的多态性,应用MVR-PCR ( Minisatellite Variant Repeat-Polymerase Chain Reaction)方法和聚丙烯酰胺梯度凝胶电泳银染法对124名河北汉人无关个体D7S21基因座进行了快速检测,并进行数字编码。每一个体平均得到36个数字编码,未发现任何两个无关个体所有编码相同,两无关个体36个编码相同的概率为3.48×10-18。三种重复单位a型、t型和0型出现的概率分别为：48.5 ％、49.4％和 2.1％。该基因座杂合度为0.9876,非父排除率为0.9746,多态性信息含量为0.9872。研究表明,D7S21基因座在河北汉族人群中具有高度的多态性,聚丙烯酰胺梯度凝胶电泳银染法简便、快速,具有一定的实用价值。 Abstract:To study the polymorphism at D7S21 locus in Hebei Han population,124 unrelated individuals were detected rapidly by Minisatellite Variant Repeat-Polymerase Chain Reaction (MVR-PCR) and polyacrylamide gradient gel electrophoresis followed by silver staining,and digital codes were obtained.About 36 digital codes were obtained from each individual.No two unrelated individuals shared the same codes.The probability of identity in 36 digital codes was 3.48×10-18.The percentage of three repeat units,a-type,t-type and 0-type was 48.5%,49.4% and 2.1% respectively.The heterozygosity (H),excluding probability of paternity（EPP）and polymorphism information content（PIC）were 0.9876,0.9746and 0.9872 respectively.The results suggested that D7S21 locus has highly polymorphism in Hebei Han population.The method-polyacrylamide gradient gel electrophoresis followed by silver staining was simple,rapid and practical.     

Assignment of 35 single-copy and 17 repetitive sequence DNA probes to human chromosome 3: high-resolution physical mapping of 7 DNA probes by in situ hybridization

Thirty-five single-copy and 17 repetitive sequence DNA probes specific for human chromosome 3 were isolated from human chromosome 3-derived genomic libraries. Seven DNA clones, including three that are polymorphic for BglII or MspI, were mapped by in situ hybridization. Four probes were mapped to 3p subregions and 3 were mapped to 3q subregions. Three of the DNA sequences map to regions overlapping a segment of chromosome 3 (3p14-23) frequently deleted in small cell lung cancer cells. By Southern blot analysis on a deletion hybrid panel, we previously mapped 6 of these probes to three distinct chromosome 3 subregions. Our in situ data support these assignments and more precisely determine the localization of each clone to the following regions: D3S34 (3p14-21), D3S35 (3p21), D3S39 (3p21), D3S40 (3p12-13), D3S37 (3q21-23), and D3S36 (3q21). Clone pL84c, a low repeat sequence clone (approximately 30 copies), was mapped to the 3q21-29 subregion. These DNA clones mapped by in situ hybridization can provide useful landmarks for the ordering and localization of other clones.     

THRA1 and D17S183 flank an interval of < 4 cM for the breast-ovarian cancer gene (BRCA1) on chromosome 17q21.

In order to pinpoint the locale of the gene for early-onset familial breast and ovarian cancer (BRCA1), polymorphisms were developed within the locus for thyroid hormone receptor alpha (THRA1) and for several anonymous sequences at chromosome 17q12-q21. The THRA1 polymorphism is a dinucleotide repeat with 10 alleles and heterozygosity.79. Gene mapping in extended families with inherited, early-onset breast and ovarian cancer indicates that BRCA1 is distal to THRA1 and proximal to D17S183 (SCG43), an interval of < 4 cM. This locale excludes HER2, THRA1, WNT3, HOX2, NGFR, PHB, COLIA1, NME1, and NME2 as candidates for BRCA1 but does not exclude RARA or EDH17B. Resolving the remaining recombination events in these families by new polymorphisms in the THRA1-D17S183 interval will facilitate positional cloning of the breast-ovarian cancer gene on chromosome 17q12-q21.     

Addition of MT, D16S10, D16S4, and D16S91 to the linkage map within 16q12.1-q22.1.

A 10-point genetic linkage map of the region 16q12.1 to 16q22.1 has been constructed using the CEPH reference families. Four loci, MT, D16S10, D16S91, and D16S4, not previously localized on a multipoint linkage map, were incorporated on the map presented here. The order of loci was cen-D16S39-MT, D16S65-D16S10-FRA16B-D16S38, D16S4, D16S91, D16S46-D16S47-HP-qter. The interval between D16S10 and 4D16S38 is 3.1 cM in males and 2.3 cM in females, and contains FRA16B. The cloning strategy for FRA16B will now be based on YAC walking from D16S10 and D16S38. The location of FRA16B between D16S10 and D16S38 provides a physical reference point for the multipoint linkage map on the short arm of chromosome 16.