A Simple PCR–RFLP Method for Genetic Phase Determination in Compound Heterozygotes

When susceptibility to diseases is caused by cis-effects of multiple alleles at adjacent polymorphic sites, it may be difficult to assess with confidence the genetic phase and identify individuals carrying the risk haplotype. Experimental assessment of genetic phase is still challenging and most population studies use statistical approaches to infer haplotypes given the observed genotypes. While these statistical approaches are powerful and have been proven very useful in large scale genetic population studies, they may be prone to errors in studies with small sample size, especially in the presence of compound heterozygotes. Here, we describe a simple and novel approach using the popular PCR–RFLP based strategy to assess the genetic phase in compound heterozygotes. We apply this method to two extensively studied SNPs in two clustered immune-related genes: The −308 (G > A) and the +252 (A > G) SNPs of the tumor necrosis factor (TNF) alpha and the lymphotoxin alpha (LTA) genes, respectively. Using this method, we successfully determined the genetic phase of these two SNPs in known compound heterozygous individuals and in every sample tested. We show that the A allele of TNF −308 is carried on the same chromosome as the LTA +252(G) allele

Interleukin-10 (IL-10) Pathway: Genetic Variants and Outcomes of HIV-1 Infection in African American Adolescents

promoter sequence have been reported to influence pathogenesis or acquisition of HIV-1 infection. T-cell increased by 31±0.9% and 17±8% every 3 months for AA and AG genotype, respectively. gene family to HIV-1/AIDS

Multiple Hits for the Association of Uterine Fibroids on Human Chromosome 1q43

<div><p>Uterine leiomyomas (or fibroids) are the most common tumors in women of reproductive age. Early studies of two familial cancer syndromes, the multiple cutaneous and uterine leiomyomatosis (MCUL1), and the hereditary leiomyomatosis and renal cell cancer (HLRCC), implicated <i>FH</i>, a gene on chromosome 1q43 encoding the tricarboxylic acid cycle fumarate hydratase enzyme. The role of this metabolic housekeeping gene in tumorigenesis is still a matter of debate and pseudo-hypoxia has been suggested as a pathological mechanism. Inactivating <i>FH</i> mutations have rarely been observed in the nonsyndromic and common form of fibroids; however, loss of heterozygosity across <i>FH</i> appeared as a significant event in the pathogenesis of a subset of these tumors. To assess the role of <i>FH</i> and the linked genes in nonsyndromic uterine fibroids, we explored a two-megabase interval spanning <i>FH</i> in the NIEHS Uterine fibroid study, a cross-sectional study of fibroids in 1152 premenopausal women. Association mapping with a dense set of single nucleotide polymorphisms revealed several peaks of association (p = 10⁻²–8.10⁻⁵) with the risk and/or growth of fibroids. In particular, genes encoding factors suspected (cytosolic FH) or known (EXO1 - exonuclease 1) to be involved in DNA mismatch repair emerged as candidate susceptibility genes whereas those acting in the autophagy/apoptosis (<i>MAP1LC3C</i> - microtubule-associated protein) or signal transduction (<i>RGS7</i> - Regulator of G-protein and <i>PLD5</i>– Phospoholipase D) appeared to affect tumor growth. Furthermore, body mass index, a suspected confounder altered significantly but unpredictably the association with the candidate genes in the African and European American populations, suggesting the presence of a major obesity gene in the studied region. With the high potential for occult tumors in common conditions such as fibroids, validation of our data in family-based studies is needed.</p></div

Colocalization of human traits of potential relevance to uterine fibroids on human chromosome 1q43.

<p>Genomic map of a 2 megabase-long interval spanning the fumarate hydratase (<i>FH</i>) gene and showing the position of specific microsatellite markers (vertical bars) and gene loci linked or associated with diseases or traits of relevance to hormone-dependent tumors such as uterine leiomyomas. QFS (Quebec family study); SHBG (sex hormone binding globulin); HERITAGE (HERITAGE family study). Other details are as described in Fig. 1.</p

Association of chromosome 1q43 single nucleotide polymorphisms with the growth of uterine leiomyomas (affected-only design and full models).

<p>P-values are derived from polytomous logistic regression models with adjustment for the covariates as described in Fig. 2.</p

Fine Mapping of the Body Fat QTL on Human Chromosome 1q43

<div><p>Introduction</p><p>Evidence for linkage and association of obesity-related quantitative traits to chromosome 1q43 has been reported in the Quebec Family Study (QFS) and in populations of Caribbean Hispanic ancestries yet no specific candidate locus has been replicated to date.</p><p>Methods</p><p>Using a set of 1,902 single nucleotide polymorphisms (SNPs) genotyped in 525 African American (AA) and 391 European American (EA) women enrolled in the NIEHS uterine fibroid study (NIEHS-UFS), we generated a fine association map for the body mass index (BMI) across a 2.3 megabase-long interval delimited by <i>RGS7</i> (regulator of G-protein signaling 7) and <i>PLD5</i> (Phospholipase D, member 5). Multivariable-adjusted linear regression models were fitted to the data to evaluate the association in race-stratified analyses and meta-analysis.</p><p>Results</p><p>The strongest associations were observed in a recessive genetic model and peaked in the 3’ end of <i>RGS7</i> at intronic rs261802 variant in the AA group (p = 1.0 x 10⁻⁴) and in meta-analysis of AA and EA samples (p = 9.0 x 10⁻⁵). In the EA group, moderate associations peaked at rs6429264 (p = 2.0 x 10⁻³) in the 2 Kb upstream sequence of <i>RGS7</i>. In the reference populations for the European ancestry in the 1,000 genomes project, rs6429264 occurs in strong linkage disequilibrium (D’ = 0.94) with rs1341467, the strongest candidate SNP for total body fat in QFS that failed genotyping in the present study. Additionally we report moderate associations at the 3’ end of <i>PLD5</i> in meta-analysis (3.2 x 10⁻⁴ ≤ p ≤ 5.8 x 10⁻⁴).</p><p>Conclusion</p><p>We report replication data suggesting that <i>RGS7</i>, a gene abundantly expressed in the brain, might be a putative body fat QTL on human chromosome 1q43. Future genetic and functional studies are required to substantiate our observations and to potentially link them to the neurobehavioral phenotypes associated with the <i>RGS7</i> region.</p></div

Association of chromosome 1q43 single nucleotide polymorphisms with the risk of uterine leiomyomas

<p>(<b>full models</b>)<b>.</b> P-values are from dichotomous logistic regression models adjusted for age, age at menarche, parity, physical activity and body mass index (BMI). BMI and physical activity were modeled as four-level variables and age at menarche and parity as two-level variables. Other details are as described in Fig. 1.</p

Association of chromosome 1q43 single nucleotide polymorphisms with the risk of uterine leiomyomas (unadjusted models).

<p>P-values for 2 d.f. tests from dichotomous logistic regression models adjusted for the only effect of age are reported separately for the African Americans (AA) and European Americans (EA) study groups. Because of the high correlations among the tightly linked SNPs, the p-values are not corrected for multiple testing. The placement of the genes in the gene map shown above the plot and the coordinates show below were derivedthe Human Genome assembly 19. Arrows indicate the orientation of the genes and are drawn proportionally to the size of the genes. <i>RGS7</i> (regulator of Gprotein 7); <i>FH</i> (fumarate hydratase); <i>KMO</i> (kynurenine 3monooxygenase); <i>OPN3</i> (opsin 3); <i>WDR64</i> (WD repeat domain 64); <i>EXO1</i> (exonuclease 1); <i>MAP1LC3C (</i>microtubuleassociated protein 1 light chain 3 gamma); <i>PLD5</i> (phospholipase D family, member 5).</p