Qing Yang Huang

A genomewide linkage scan for quantitative-trait loci for obesity phenotypes.

Obesity is an increasingly serious health problem in the world. Body mass index (BMI), percentage fat mass, and body fat mass are important indices of obesity. For a sample of pedigrees that contains >10,000 relative pairs (including 1,249 sib pairs) that are useful for linkage analyses, we performed a whole-genome linkage scan, using 380 microsatellite markers to identify genomic regions that may contain quantitative-trait loci (QTLs) for obesity. Each pedigree was ascertained through a proband who has extremely low bone mass, which translates into a low BMI. A major QTL for BMI was identified on 2q14 near the marker D2S347 with a LOD score of 4.04 in two-point analysis and a maximum LOD score (MLS) of 4.44 in multipoint analysis. The genomic region near 2q14 also achieved an MLS >2.0 for percentage of fat mass and body fat mass. For the putative QTL on 2q14, as much as 28.2% of BMI variation (after adjustment for age and sex) may be attributable to this locus. In addition, several other genomic regions that may contain obesity-related QTLs are suggested. For example, 1p36 near the marker D1S468 may contain a QTL for BMI variation, with a LOD score of 2.75 in two-point analysis and an MLS of 2.09 in multipoint analysis. The genomic regions identified in this and earlier reports are compared for further exploration in extension studies that use larger samples and/or denser markers for confirmation and fine-mapping studies, to eventually identify major functional genes involved in obesity.

Mutation Patterns at Dinucleotide Microsatellite Loci in Humans

Microsatellites are a major type of molecular markers in genetics studies. Their mutational dynamics are not clear. We investigated the patterns and characteristics of 97 mutation events unambiguously identified, from 53 multigenerational pedigrees with 630 subjects, at 362 autosomal dinucleotide microsatellite loci. A size-dependent mutation bias (in which long alleles are biased toward contraction, whereas short alleles are biased toward expansion) is observed. There is a statistically significant negative relationship between the magnitude (repeat numbers changed during mutation) and direction (contraction or expansion) of mutations and standardized allele size. Contrasting with earlier findings in humans, most mutation events (63%) in our study are multistep events that involve changes of more than one repeat unit. There was no correlation between mutation rate and recombination rate. Our data indicate that mutational dynamics at microsatellite loci are more complicated than the generalized stepwise mutation models.

Searching for osteoporosis genes in the post-genome era: Progress and challenges

Osteoporosis is a common skeletal disease characterized by low bone mineral density (BMD), deterioration of bone microarchitecture and increased fracture risk. It is a complex disease that has high social and economic costs. Osteoporosis and its associated phenotypes are under the strong genetic control. Identification and characterization of specific loci or genes involved in determining osteoporosis and its associated phenotypes will contribute to a greater understanding of the pathogenesis of osteoporosis, and ultimately might lead to the development of better diagnosis, prevention and treatment strategies. Efforts to identify osteoporosis genes have focused on three approaches: animal models, candidate gene approach, and genome-wide scans. In this article, we review the current status for mapping and identification of genes for osteoporosis, with a focus on some promising regions and future prospects.

Several genomic regions potentially containing QTLs for bone size variation were identified in a whole-genome linkage scan.

Bone size is an important determinant of osteoporotic fractures. For a sample of 53 pedigrees that contains more than 10,000 relative pairs informative for linkage analyses, we performed a whole‐genome linkage scan using 380 microsatellite markers to identify genomic regions that may contain QTLs of bone size (two dimensional measurement by dual energy X‐ray absorptiometry). We conducted two‐ and multi‐point linkage analyses. Several potentially important genomic regions were identified. For example, the genomic region 17q23 may contain a QTL for wrist (ultra distal) bone size variation; a LOD score of 3.98 is achieved at D17S787 in two‐point analyses and a maximum LOD score (MLS) of 3.01 is achieved in multi‐point analyses in 17q23. 19p13 may contain a QTL for hip bone size variation; a LOD score of 1.99 is achieved at D19S226 in two‐point analyses and a MLS of 2.83 is achieved in 19p13 in multi‐point analyses. The genomic region identified on chromosome 17 for wrist bone size seems to be consistent with that identified for femur head width variation in an earlier whole‐genome scan study. The genomic regions identified in this study and an earlier investigation on one‐dimensional bone size measurement by radiography are compared. The two studies may form a basis for further exploration with larger samples and/or denser markers for confirmation and fine mapping studies to eventually identify major functional genes and the associated etiology for osteoporosis.

Confirmation linkage study in support of the X chromosome harbouring a QTL underlying human height variation

Human height is a complex trait determined by both genetic and environmental factors. An initial whole genome study showed several genomic regions with suggestive linkage to height in a sample of 630 subjects from 53 human pedigrees. The present study was conducted in an extended sample of 1816 subjects from 79 pedigrees in an attempt to replicate and confirm the results of the previous whole genome scan. Xq24–25 on the X chromosome was confirmed as the region suggestive of linkage to height. In the previous whole genome study, a microsatellite marker of the region DXS1001 achieved a two point LOD score of 1.91 for linkage to height. In the present study on the 79 pedigrees, another marker of the same region, DXS8067, which is only 2.7 cM away from the former marker, attained a higher two point LOD score of 2.66. Moreover, the region’s significant linkage to height was sustained, with a two point LOD score of 1.00 achieved in a subset of the current sample (1026 subjects from 26 new pedigrees), which is independent of the original 630 subjects used in the whole genome study. Our results—together with identification of several syndromes with short stature, which are in linkage to Xq24–25—strongly suggest that this region may harbour a quantitative trait locus (QTL) underlying human height variation.nnHuman height is a typical complex trait determined by both genetic and environmental factors. Nutritional status and diseases are the most important environmental factors controlling human linear growth.1–4 However, genetic factors play a more dominant role in height determination. This is indicated by a significant familial aggregation of the trait, translating into a heritability of well above 50%.5–9nnThe search for genes underlying height variation has long been an endeavour in the field of genetic studies of complex traits. …

Linkage and association of the CA repeat polymorphism of the IL6 gene, obesity-related phenotypes, and bone mineral density (BMD) in two independent Caucasian populations

AbstractGenetic factors play an important role in osteoporosis and obesity, two serious public health problems in the world. We investigated the relationships between obesity-related phenotypes, bone mineral density (BMD) and the CA repeat polymorphism of the IL6 gene in two large independent samples using the quantitative transmission disequilibrium test (QTDT). The first sample consisted of 1,816 individuals from 79 multigenerational pedigrees. Each pedigree was identified through a proband with BMD Z-scores ≤−1.28 at the hip or spine. The second sample was a randomly ascertained set of 636 individuals from 157 nuclear families. Ten alleles containing 9–18 CA repeats were identified in our Caucasian populations. For body mass index (BMI), fat mass and percentage fat mass (PFM), highly significant (P<0.01) or significant (P<0.05) results were found for linkage in our sample of nuclear families and for association in the multigenerational pedigrees. We also observed weak evidence for linkage (P=0.069) with spine BMD and for association with hip BMD in the sample of multigenerational pedigrees. Our results suggest that genetic variation in or near the IL6 locus may be involved in the etiology of obesity and osteoporosis.

A second-stage genome scan for QTLs influencing BMD variation.

Low bone mineral density (BMD) is a major risk factor for osteoporotic fracture. To identify genomic regions harboring quantitative trait loci (QTLs) contributing to BMD variation, we performed a two-stage genome screen. The first stage involved genotyping of a sample of 53 pedigrees with 630 individuals using 400 microsatellite markers spaced at approximately 10-cM intervals throughout the genome. Ten genomic regions with multi- and/or two-point LOD scores greater than 1.5 were observed. In the present second-stage study, 60 microsatellite markers, with a mean spacing of about 5xa0cM, were genotyped in these regions in an expanded sample of 79 pedigrees that contained 1816 subjects. Each pedigree was ascertained through a proband with extreme BMD at the hip or spine. BMD at the spine (L1–4), hip (the femoral neck, trochanter, and intertrochanteric region), and wrist (the ultradistal region) was measured by dual-energy X-ray absorptiometry (DXA) and was adjusted for age, sex, height, and weight. Two-point and multipoint linkage analyses were performed for each BMD site using statistical genetic methods that are implemented in the computer package SOLAR. Several regions (7q11, 10q26, 12q13, and 12q24) achieved LOD scores in excess of 1 in the second-stage followup study. The current results replicate some of our previous linkage findings and also highlight some of the difficulties facing microsatellite linkage mapping for complex human diseases.

Linkage and Association Between CA Repeat Polymorphism of the TNFR2 Gene and Obesity Phenotypes in Two Independent Caucasian Populations

Previously, our group has reported a suggestive linkage evidence of 1p36 with body mass index (BMI) (LOD = 2.09). The tumor necrosis factor receptor 2 (TNFR2) at 1p36 is an excellent positional and functional candidate gene for obesity. In this study, we have investigated the linkage and association between the TNFR2 gene and obesity phenotypes in two large independent samples, using the quantitative transmission disequilibrium tests (QTDT). The first group was made up of 1,836 individuals from 79 multi-generation pedigrees. The second group was a randomly ascertained set of 636 individuals from 157 US Caucasian nuclear families. Obesity phenotypes tested include BMI, fat mass, and percentage fat mass (PFM). A significant result (P = 0.0056) was observed for linkage with BMI in the sample of the multigenerational pedigrees. Our data support the TNFR2 gene as a quantitative trait locus (QTL) underlying BMI variation in the Caucasian populations.