N-ras-like sequences on chromosomes 9, 6 and 22 with a polymorphism at the chromosome 9 locus

Two clones, pCN1 and pCN2, which together form full-length cDNA for N- ras , were used to search for restriction fragment length polymorphisms. pCN2, which entirely consists of 3' non-translated sequences, revealed more bands on DNA transfer hybridizations than could be accounted for using the known restriction map of N- ras. None of the extra cross hybridizing sequences is located on chromosome 1. One of these sequences showed a high-frequency two-allele polymorphism with the restriction enzyme Taq I and maps to the short arm of chromosome 9. Of the remaining two sequences, one maps to chromosome 22 and the other maps to the short arm of chromosome 6. pCN1A, which contains the 5' untranslated regions and all the coding exons of N- ras only hybridized to the chromosome 1 site. No polymorphisms have been found for pCN1 with Taq I, Msp I, Bcl I, Bgl I, EcoR I, Bst XI, Xba I, Bam HI, Bgl II or Hind III.     

Dinucleotide repeat polymorphism on chromosome 9q32

Summary A new microsatellite was developed from a cosmid clone (cCI9-246) assigned to human chromosome 9q32.     

Identification of a locus (LCA9) for Leber's congenital amaurosis on chromosome 1p36

Leber's congenital amaurosis (LCA) is the most common cause of inherited childhood blindness and is characterised by severe retinal degeneration at or shortly after birth. We have identified a new locus, LCA9, on chromosome 1p36, at which the disease segregates in a single consanguineous Pakistani family. Following a whole genome linkage search, an autozygous region of 10 cM was identified between the markers D1S1612 and D1S228. Multipoint linkage analysis generated a lod score of 4.4, strongly supporting linkage to this region. The critical disease interval contains at least 5.7 Mb of DNA and around 50 distinct genes. One of these, retinoid binding protein 7 (RBP7), was screened for mutations in the family, but none was found.     

Rat chromosome 9 bears a major susceptibility locus for IgE response

Injection of Brown Norway (BN) rats with gold salts provides a model to analyze the genetic control of the IgE response. A cohort of F2 progeny of susceptible BN and resistant LEW strains has been studied to carry out a genome-wide search for loci controlling the IgE response. Genome scanning identified two previously described loci, Atps1 and Atps2, and a new locus, Atps3. Atps1 linked to the MHC and Atps2 linked to the cytokine gene cluster that included the IL-4 region have been previously associated with serum IgE concentrations and with other Th2-dependent immune manifestations triggered by gold salts. The new interval, Atps3, identified on chromosome 9 (Lod score = 16), appears to play a major role in the control of the IgE response since it accounts for 31% of the genetic variance. Moreover, Atps3 is linked to anti-laminin antibody response and to glomerular immunoglobulin deposits. The identification and functional characterization of genes involved in these regions, particularly in Atps3, may shed light on the pathogenesis of atopic diseases in man.     

Identification of markers flanking the tuberous sclerosis locus on chromosome 9 (TSC1).

Analysis of a large tuberous sclerosis pedigree confirmed linkage to a locus on the long arm of chromosome 9, with recombination events placing the disease gene distal to gelsolin and proximal to dopamine beta-hydroxylase.     

DFNB79: reincarnation of a nonsyndromic deafness locus on chromosome 9q34.3

Genetic analysis of an inbred Pakistani family PKDF280, segregating prelingual severe to profound sensorineural hearing loss, provided evidence for a DFNB locus on human chromosome 9q34.3. Co-segregation of the deafness trait with marker D9SH159 was determined by a two-point linkage analysis (LOD score 9.43 at θ=0). Two additional large families, PKDF517 and PKDF741, co-segregate recessive deafness with markers linked to the same interval. Haplotype analyses of these three families refined the interval to 3.84 Mb defined by D9S1818 (centromeric) and D9SH6 (telomeric). This interval overlaps with the previously reported DFNB33 locus whose chromosomal map position has been recently revised and assigned to a new position on chromosome 10p11.23–q21.1. The nonsyndromic deafness locus on chromosome 9q segregating in family PKDF280 was designated DFNB79. We are currently screening the 113 candidate DFNB79 genes for mutations and have excluded CACNA1B, EDF1, PTGDS, EHMT1, QSOX2, NOTCH1, MIR126 and MIR602.     

Assignment of a locus for dominantly inherited venous malformations to chromosome 9p

Venous malformation is the most common type of vascular anomaly.Depending upon size and location, these slow-flow anomaliesmay cause pain, anatomic distortion, or threaten life. Mostvenous malformations occur sporadically and present as solitarylesions. They also occur in several syndromes, some of whichdemonstrate Mendelian inheritance. We have mapped the locusfor an autosomal dominant disorder in a three generation familythat manifests as multiple cutaneous and mucosal venous malformations.This locus lies within a 24 cM interval on chromosome 9p, definedby the markers D9S157 and D9S163. The     

The chromosome 9 ALS and FTD locus is probably derived from a single founder

We and others have recently reported an association between amyotrophic lateral sclerosis (ALS) and single nucleotide polymorphisms on chromosome 9p21 in several populations. Here we show that the associated haplotype is the same in all populations and that several families previously shown to have genetic linkage to this region also share this haplotype. The most parsimonious explanation of these data are that there is a single founder for this form of disease.     

中国汉族人群中TNF-α基因多态性与血脂关系的研究

目的研究肿瘤坏死因子-α(TNF-α)基因多态性与健康人群血脂谱改变的关系.方法随机选择182例湖北地区无血缘关系健康汉族人群,用聚合酶链反应限制性片段长度多态性(PCR-RFLP)技术检测其TNF-α基因多态性,分析各基因型对血脂、脂蛋白、栽脂蛋白的影响.结果TNF-α-238位点基因型在中国正常人群中的分布仅与日本人群中的分布较为接近,TNF-α-863位点基因型的分布与日本人、高加索人中的分布差异无显著性.结论在汉族人群中存在TNF-α基因多态性,且与血脂水平无相关性(P＞0.05).     

IDDM9 and a locus for rheumatoid arthritis on chromosome 3q appear to be distinct.

Markers near a locus for type 1 diabetes on chromosome 3q22-q25 (IDDM9) demonstrate linkage to rheumatoid arthritis, however it is not clear whether these two loci overlap. Sex-specific linkage analysis may be of interest for rheumatoid arthritis on chromosome 3q since linkage of type 1 diabetes to IDDM9 derives predominantly from affected female sibpairs, and rheumatoid arthritis is more common in females than males. Using data from a recent genome scan for rheumatoid arthritis and sex-specific linkage analysis we show that linkage of rheumatoid arthritis to chromosome 3q peaks approximately 30 cM centromeric to IDDM9. Furthermore, there is no evidence for linkage to IDDM9 in females with rheumatoid arthritis.     

Juvenile hemochromatosis locus maps to chromosome 1q in a French Canadian population

Juvenile hemochromatosis (JH) is a rare autosomal recessive disorder that causes iron overload. In the French Canadian region of Saguenay Lac-Saint-Jean the worldwide largest cohort of JH cases has been identified. Here, we report the mapping of this large cohort of cases to the HFE2 locus on chromosome 1q. A maximum multipoint location score of 7.02 was observed with marker D1S2344. A common ancestral haplotype, showing the presence of a founder effect, was identified. The analysis of recombinants allowed us to confirm the JH candidate region.     

Linkage studies suggest a possible locus for developmental dyslexia on chromosome 1p.

Eight extended dyslexic families with at least four affected individuals were genotyped with twelve genetic markers spanning the Rh (rhesus factor) locus. Eleven of these markers were located on the short arm and the other was on the long arm of chromosome 1. Five theoretically derived phenotypes were used in the linkage analyses: 1) phonemic awareness; 2) phonological decoding; 3) rapid automatized naming; 4) single word reading; and 5) vocabulary. In addition, a lifetime diagnosis of dyslexia was used as a phenotype. Both parametric and non-parametric genetic analyses were completed. The results supported the importance of a putative locus on 1p. In addition, two-locus analyses assuming the interaction between a 1p locus and a 6p locus, previously shown to be of interest for dyslexia, were conducted. As a result, the nonparametric linkage (NPL) scores for rapid automatized naming and phonological decoding were significantly increased. In particular, the NPL scores for rapid automatized naming exceeded 5.0 for certain markers. These results provide strong evidence for separate but jointly acting contributions of the 1p and 6p loci to the reading impairments associated with rapid naming and suggestive evidence for a similar mechanism involving phonological decoding.     

CGH-targeted linkage analysis reveals a possible BRCA1 modifier locus on chromosome 5q

Women with germline mutations in BRCA1 have a greatly elevated risk of breast and ovarian cancer. However, considerable variation in the degree of breast cancer risk associated with a BRCA1 mutation has been observed, suggesting that modifiers of BRCA1 penetrance may exist. We hypothesized that the modifier genes might be located in regions of allelic imbalance in the tumors of BRCA1 mutation carriers, as have been reported on chromosomes 4p, 4q and 5q. In order to determine whether novel genetic modifiers of BRCA1-associated breast cancer penetrance in these regions exist, we used non-parametric linkage analysis methods to determine whether allele sharing of chromosomes 4p, 4q and 5q was observed preferentially within BRCA1 mutation families in women with BRCA1 mutations and breast cancer. No significant linkage on chromosome 4p or 4q was observed associated with breast cancer risk in BRCA1 mutation carriers. However, we observed a significant linkage signal at D5S1471 on chromosome 5q (P = 0.009) in all the families analyzed together. The significance of this observation increased in the subset of families with an average of breast cancer diagnosis less than 45 years (P = 0.003). These results suggest the presence of one or more genes on chromosome 5q33-34 that modify breast cancer risk in BRCA1 mutation carriers. The approach described here may be utilized to identify penetrance modifiers in other autosomal dominant syndromes.     

Association of single-nucleotide polymorphism on chromosome 9 and ischemic stroke in Heilongjiang province in China

There is a significant correlation between ischemic stroke (IS) and chromosome 9. However, its status was uncertain in China’s cold regions. 1920 IS patients, and 1920 healthy individuals were included in the study. Blood samples were collected. The association of SNPs with IS was evaluated by Sequenom, and logistic regression models adjusted for known risk factors of IS were constructed to assess the SNPs’ associations in cases and controls. We found rs1333040 and rs2383207 were associated with IS, compared with primitive genotypes. The genotype CT of rs7027526 has a protective role during IS development, while the effect of the genotype TT is still not clear. These results changed after stratification by age and sex. In conclusion, rs1333040 and rs2383207 SNPs in CDKN2BAS are associated with ischemic stroke in the Chinese Han population. This study confirms the association between 9p21.3 and IS.     

Non-syndromic recessive deafness in Jordan: mapping of a new locus to chromosome 9q34.3 and prevalence of DFNB1 mutations

Non-syndromic recessive deafness (NSRD) is the most commonly encountered form of hereditary hearing loss. The majority of NSRD cases in the Mediterranean area are linked to the DFNB1 locus (the connexin 26 GJB2 gene). Unrelated NSRD patients issued from 68 Jordanian families, were tested for mutations of the GJB2 gene by sequencing. Sixteen per cent of the families tested were linked to the DFNB1 locus. The 35delG was the only GJB2 mutation detected in these families. One of these families, presenting with four affected members and not linked to the gene, was subjected to a genome-wide search and was found to be mapped to 9q34.3 with a multipoint lodscore of 3.9. One candidate gene in the interval, coding for the chloride intracellular channel 3, CLIC3, was tested and excluded. The identification of a new NSRD locus, DFNB33, in one Jordanian family, shows the wide genetic heterogeneity that characterizes hearing impairment and the genetic diversity in Middle-Eastern populations.     

Expression of GALT in 9p chromosome alterations: assignment of GALT locus to 9cen→9p22

Determination of activity and electrophoretic mobility of GALT in patients with various chromosome 9 deletions and duplications confirms the assignment of its locus to 9p and suggests its locus is in the segment 9cen→p22. Two inversions of 9qh (inv(9)(pllql2)) did not alter GALT expression.