A novel founder MSH2 deletion in Ethiopian Jews is mainly associated with early-onset colorectal cancer

Lynch syndrome is an inherited cancer predisposition syndrome caused by germline defects in any of the mismatch repair (MMR) genes. Diagnosis of carriers makes precision prevention, early detection, and tailored treatment possible. Herein we report a novel founder deletion of 18,758 bp, mediated by Alu repeats on both sides, detected in Ethiopian Jews. The deletion, which encompasses exon 9-10 of the MSH2 coding sequence, is associated mainly with early-onset MSH2/MSH6-deficient colorectal cancer (CRC) and liposarcoma. Testing of 35 members of 5 seemingly unrelated families of Ethiopian origin yielded 10/21 (48%) carriers, of whom 9 had CRC. Age at first tumor diagnosis ranged from 16 to 89 years. Carriers from the oldest generations were diagnosed after age 45 years (mean 57), and carriers from the younger generation were diagnosed before age 45 years (mean 30). Awareness of this founder deletion is important to improve patient diagnosis, institute surveillance from an early age, and refer patients for genetic counseling addressing the risk of bi-allelic constitutional MMR deficiency syndrome.

Genetics of schizophrenia in the South African Xhosa

Africa, the ancestral home of all modern humans, is the most informative continent for understanding the human genome and its contribution to complex disease. To better understand the genetics of schizophrenia, we studied the illness in the Xhosa population of South Africa, recruiting 909 cases and 917 age-, gender-, and residence-matched controls. Individuals with schizophrenia were significantly more likely than controls to harbor private, severely damaging mutations in genes that are critical to synaptic function, including neural circuitry mediated by the neurotransmitters glutamine, γ-aminobutyric acid, and dopamine. Schizophrenia is genetically highly heterogeneous, involving severe ultrarare mutations in genes that are critical to synaptic plasticity. The depth of genetic variation in Africa revealed this relationship with a moderate sample size and informed our understanding of the genetics of schizophrenia worldwide.

Alpha-thalassemia intellectual disability: variable phenotypic expression among males with a recurrent nonsense mutation - c.109C>T (p.R37X)

Alpha-thalassemia intellectual disability, one of the recognizable X-linked disability syndromes, is characterized by short stature, microcephaly, distinctive facies, hypotonic appearance, cardiac and genital anomalies, and marked skewing of X-inactivation in female carriers. With the advent of next generation sequencing, mutations have been identified that result in less severe phenotypes lacking one or more of these phenotypic manifestations. Here we report five unrelated kindreds in which a c.109C>T (p.R37X) mutation segregates with a variable but overall milder phenotype. The distinctive facial appearance of alpha-thalassemia intellectual disability was present in only one of the 18 affected males evaluated beyond the age of puberty, although suggestive facial appearance was present in several during infancy or early childhood. Although the responsible genetic alteration is a nonsense mutation in exon 2 of ATRX, the phenotype appears to be partially rescued by the production of alternative transcripts and/or other molecular mechanisms.

Abstract P3-07-05: Frequent BRCA1 and BRCA2 mutations are found in Mexican and Mexican-American women with breast cancer

Background: The Arizona Cancer Registry has shown that in Pima County, AZ, breast cancer diagnosed in young Latinas increased 40% from 2004-2008, compared to 1999-2003, and Latinas more likely to die of their cancer. This study seeks to characterize genetic variation in women of Mexican ancestry with breast cancer using next generation sequencing, with the goal of providing prevalence information to help guide screening and cancer prevention efforts.

Methods: The ELLA Binational Breast Cancer Study enrolled women of Mexican ancestry living in either U.S. or Mexico within 24 months of breast cancer diagnosis. Mexican women from the state of Jalisco were collected through collaboration with the Universidad de Guadalajara and women of Mexican ancestry were recruited from Tucson and Phoenix, AZ. Genomic DNA from 92 ELLA study participants (49 from the U.S. and 43 from Mexico) was enriched for breast cancer influencing gene sequence using the BROCA panel with standard techniques. Samples were sequenced with next generation sequencing and variants identified.

Results: Sequencing of breast cancer risk genes in 92 Mexican and Mexican-American women with breast cancer revealed the presence of deleterious mutations in 15% of women (14/92). Five carry mutations in BRCA1, 5 in BRCA2, 2 in CHEK2, 1 in PALB2 and 1 in RAD51C. An additional 9% of participants (8/92) carry rare mutations of unknown functional consequence in the same genes. Four carry mutations in BRCA1 or BRCA2 at sites predicted to alter splice enhancers and four carry missense mutations in CHEK2 that are predicted to damage to kinase function. None of these variants appear in public databases or are characterized functionally in gene-specific databases. Dozens of women carry VUS or novel variants.

Women carrying BRCA1 mutations are significantly more likely to have had triple negative pathology. Women carrying other mutations known or thought to be deleterious are also more likely to have been younger at diagnosis, to have more aggressive breast cancer or to report a family history of breast cancer.

Table 1. Deleterious MutationsGeneEffectTotalBRCA1185delAG1BRCA12569delC2BRCA1Del Complete Gene1BRCA1Del Exons 9-121BRCA2c.658delGT1BRCA2c.3264insT2BRCA2c.5195delT1BRCA2c.6024insG1CHEK2R160G2PALB2S779 Stop1RAD51CDel Exons 4-91

Conclusion: Deleterious BRCA1 and BRCA2 gene mutations are common among women of Mexican ancestry diagnosed with breast cancer. Within this cohort, the prevalence of BRCA1/2 mutations is 11%, and 4% of women carry mutations in other genes increasing breast cancer risk. This is higher than the 10% mutation prevalence estimated for Ashkenazi Jewish women with breast cancer. An additional 9% of women carry variants likely to disrupt gene function and dozens of VUS and novel variants are found in these women. Further analysis of samples from the remaining 942 women using genetic sequencing will help further elucidate the role of genetic risk factors in women of Mexican ancestry with breast cancer.

Citation Information: Cancer Res 2013;73(24 Suppl): Abstract nr P3-07-05.

A truncating mutation in GPSM2 is associated with recessive non-syndromic hearing loss

Hereditary deafness is a genetically heterogeneous phenotype for which more than 100 genomic loci have been identified thus far. By analysis of a consanguineous Palestinian family, GPSM2 was recently discovered to be the cause of autosomal recessive non-syndromic hearing loss DFNB82. Here, we report a second truncating mutation, GPSM2 p.Q562X, identified via autozygosity mapping in a consanguineous Turkish family. This report provides evidence for allelic heterogeneity of GPSM2 and confirms its causative role for non-syndromic deafness.

Comparison of the Simplify D-dimer assay performed at the bedside with a laboratory-based quantitative D-dimer assay for the diagnosis of pulmonary embolism in a low prevalence emergency department population

BACKGROUND

The immunofiltration D-dimer assay could allow point-of-care testing for pulmonary embolism (PE). A study was undertaken to compare a clinician-performed qualitative D-dimer assay with the automated quantitative D-dimer test.

METHODS

A prospective observational study was conducted from January to October 2005 at an urban academic emergency department (ED). 1193 patients of mean (SD) age 47 (16) years (66% female) were enrolled. The study protocol combined pretest probability estimation, D-dimer testing by both a qualitative immunochromatographic assay (Simplify) performed at the point of care by 192 different clinicians and a quantitative D-dimer test performed in a CLIA-certified laboratory. The criterion standard was image-proven PE or deep venous thrombosis within 45 days after enrollment. To test interobserver agreement for the qualitative assay, two blinded observers independently read 841 Simplify cartridges.

RESULTS

Of 1193 patients enrolled, 45 were PE+ (3.8%, 95% CI 2.8% to 5.0%). Qualitative results were available for 1169 (98%) and quantitative results were available for 1136 (95%). Comparison of the qualitative and quantitative D-dimer tests gave the following results: sensitivity 91% (95% CI 78% to 98%) vs 93% (95% CI 80% to 98%); specificity 57% (95% CI 54% to 60%) vs 57% (95% CI 54% to 60%); likelihood ratio negative 0.16 (95% CI 0.06 to 0.37) vs 0.13 (95% CI 0.05 to 0.35). The weighted Cohen's kappa for interpretation of the qualitative assay was 0.69 (95% CI 0.63 to 0.76).

CONCLUSIONS

In this very low-risk ED population, a qualitative D-dimer assay performed at the point of care had similar diagnostic accuracy to the quantitative D-dimer test. Interobserver agreement for the qualitative test was good.

The effects of cattle sex on carcass characteristics and longissimus muscle palatability

Two experiments were conducted to determine the effects of sex on carcass traits and cooked beef steak palatability. In Exp. 1, steers (n = 99), heifers (n = 51), and intravaginally spayed heifers (n = 46) were fed a high-energy diet for 161 d. No implants were administered, and heifers were not fed melengestrol acetate to suppress estrus. In Exp. 2, 60 steers and 60 intact heifers from the same ranch source used in Exp. 1 were fed in 2 locations (sites 1 and 2). All management factors were equal across experiments except that intact heifers were fed melengestrol acetate to suppress estrus in Exp. 2. Steers in Exp. 1 were 25 kg heavier (P < 0.01) in HCW than heifers at comparable (P = 0.39) carcass fat thickness. Spayed heifers (Exp. 1) had a 5.7% smaller (P < 0.05) LM area compared with steers and intact heifers, which were similar. In Exp. 2, there was no difference (P = 0.2) in carcass weight, and heifers had greater (P < 0.01) 12th rib fat thickness compared with steers. Calculated yield grades were similar (P = 0.21) among treatments in Exp. 1 and tended (P = 0.08) to be greater for heifers compared with steers in Exp. 2. In Exp. 1, USDA quality grades and marbling scores were lower (P < 0.01) for steers compared with intact and spayed heifers, which were similar. The effects of sex on tenderness were examined at a common level of fat-thickness and marbling by covariate analysis. Steaks from steers, compared with those from nonimplanted, intact heifers, in the 2 experiments combined were: (a) superior (P < 0.05) in 2 of 9 palatability assessments when subcutaneous fat thickness (at the 12th rib) was adjusted to a common level, and (b) superior (P < 0.05) in 6 of 9 palatability assessments when marbling score was adjusted to a common level. In Exp. 1, steaks from nonimplanted steers compared with those from nonimplanted spayed heifers were: (a) superior (P < 0.05) in 0 of 8 palatability assessments when subcutaneous fat thickness (at the 12th rib) was adjusted to a common level, and (b) superior (P < 0.05) in 3 of 8 palatability assessments when marbling score was adjusted to a common level. These findings suggest that sex should be added to the list of antemortem factors contributing to variation in cooked beef steak tenderness. However, more research is needed to precisely identify those factors contributing to the lower tenderness observed for steaks from heifer carcasses.

Gene therapy for breast and ovarian cancer with BRCA1

As an initial step toward gene therapy for ovarian cancer, we conducted a Phase 1 trial to assess the pharmacokinetics and toxicity of intraperitoneal BRCA1sv retroviral vector therapy. Gene transfer and expression were documented by PCR, southern blot, RT-PCR and nuclease protection assays. Pharmacokinetics were assessed by PCR and southern blots detecting vector DNA, and toxicity was evaluated by clinical exam and fluid analysis. Three of twelve patients developed an acute sterile peritonitis which spontaneously resolved within 48 hours. Plasma and peritoneal antibodies to the retroviral envelope protein were detected only in patients treated with the highest dose levels but not in others, despite repeat dosing for an interval of up to four months. Eight patients showed stable disease for 4 to 16 weeks. Three patients showed tumor reduction with diminished miliary tumor implants at reoperation (two patients) and radiographic shrinkage of measurable disease (one patient). Ovarian cancer may provide an imporant model for retroviral gene therapy studies due to vector stability, minimal antibody response, and access to tumor by intraperitoneal therapy.

A functional assay for mutations in tumor suppressor genes caused by mismatch repair deficiency

The coding sequences of multiple human tumor suppressor genes include microsatellite sequences that are prone to mutations. Saccharomyces cerevisiae strains deficient in DNA mismatch repair (MMR) can be used to determine de novo mutation rates of these human tumor suppressor genes as well as any other gene sequence. Microsatellites in human TGFBR2, PTEN and APC genes were placed in yeast vectors and analyzed in isogenic yeast strains that were wild-type or deletion mutants for MSH2 or MLH1. In MMR-deficient strains, the vector containing the (A)(10) microsatellite sequence of TGFBR2 had a mutation rate (mutations/cell division) of 1.4 x 10(-4), compared to a mutation rate of 1.7 x 10(-6) in the wild-type strain. In MMR-deficient strains, mutation rates in PTEN and APC were also elevated above background levels. PTEN mutation rates were higher in both msh2 (4.4 x 10-5) and mlh1 strains (2.3 x 10-5). APC mutation rates in the msh2 strain (2.4 x 10-6) and the mlh1 strain (1.7 x 10-6) were also significantly, but less dramatically, elevated over background. Mutations selected for in the yeast screen were identical to those previously observed in human tumor samples with microsatellite instability (MSI). This functional assay has applicability in providing quantitative data about microsatellite mutation rates caused by MMR deficiency in any human tumor suppressor gene sequence. It can also be applied as a genetic screen to identify new genes that are vulnerable to such microsatellite mutations and thus may be involved in the neoplastic development of tumors with MSI.

Tamoxifen and breast cancer incidence among women with inherited mutations in BRCA1 and BRCA2: National Surgical Adjuvant Breast and Bowel Project (NSABP-P1) Breast Cancer Prevention Trial

CONTEXT

Among cancer-free women aged 35 years or older, tamoxifen reduced the incidence of estrogen receptor (ER)-positive but not ER-negative breast cancer. The effect of tamoxifen on breast cancer incidence among women at extremely high risk due to inherited BRCA1 or BRCA2 mutations is unknown.

OBJECTIVE

To evaluate the effect of tamoxifen on incidence of breast cancer among cancer-free women with inherited BRCA1 or BRCA2 mutations.

DESIGN, SETTING, AND PARTICIPANTS

Genomic analysis of BRCA1 and BRCA2 for 288 women who developed breast cancer after entry into the randomized, double-blind Breast Cancer Prevention Trial of the National Surgical Adjuvant Breast and Bowel Project (between April 1, 1992, and September 30, 1999).

MAIN OUTCOME MEASURE

Among women with BRCA1 or BRCA2 mutations, incidence of breast cancer among those who were receiving tamoxifen vs incidence of breast cancer among those receiving placebo.

RESULTS

Of the 288 breast cancer cases, 19 (6.6%) inherited disease-predisposing BRCA1 or BRCA2 mutations. Of 8 patients with BRCA1 mutations, 5 received tamoxifen and 3 received placebo (risk ratio, 1.67; 95% confidence interval, 0.32-10.70). Of 11 patients with BRCA2 mutations, 3 received tamoxifen and 8 received placebo (risk ratio, 0.38; 95% confidence interval, 0.06-1.56). From 10 studies, including this one, 83% of BRCA1 breast tumors were ER-negative, whereas 76% of BRCA2 breast tumors were ER-positive.

CONCLUSION

Tamoxifen reduced breast cancer incidence among healthy BRCA2 carriers by 62%, similar to the reduction in incidence of ER-positive breast cancer among all women in the Breast Cancer Prevention Trial. In contrast, tamoxifen use beginning at age 35 years or older did not reduce breast cancer incidence among healthy women with inherited BRCA1 mutations. Whether tamoxifen use at a younger age would reduce breast cancer incidence among healthy women with BRCA1 mutations remains unknown.

BRCA1 RING domain cancer-predisposing mutations. Structural consequences and effects on protein-protein interactions

Cancer-predisposing missense mutations in the RING domain of BRCA1 primarily target Zn(2+)-liganding residues. Here we report on the structural consequences of such mutations introduced into the second Zn(2+) site (Site II) of the BRCA1 RING domain and their effect on the interaction with the BARD1 RING domain. Each of the BRCA1 Site II mutants still interact and form a stable heterodimer with BARD1. Limited proteolysis of BRCA1/BARD1 complexes, monitored by matrix-assisted laser desorption ionization time-of-flight spectrometry, show that the mutations cause a local structural perturbation that is primarily confined to the second Zn(2+) binding loop of the BRCA1 subunit. These findings are consistent with the structure of the BRCA1/BARD1 heterodimer, which shows this region is well removed from the helices required for dimerization with BARD1. Instead, the mutations alter a region of BRCA1 that appears to be required for interaction with ubiquitin-conjugating enzymes.

Non-syndromic progressive hearing loss DFNA38 is caused by heterozygous missense mutation in the Wolfram syndrome gene WFS1

Dominantly inherited progressive hearing loss DFNA38 is caused by heterozygosity for a novel mutation in WFS1, the gene for recessively inherited Wolfram syndrome. Wolfram syndrome is defined by juvenile diabetes mellitus and optic atrophy and may include progressive hearing loss and other neurological symptoms. Heterozygotes for other Wolfram syndrome mutations generally have normal hearing. Dominant deafness defined by DFNA38 is more severe than deafness of Wolfram syndrome patients and lacks any syndromic features. In a six-generation kindred from Newfoundland, Canada, WFS1 Ala716Thr (2146 G-->A) was shared by all deaf members of the family and was specific to deaf individuals. The causal relationship between this missense mutation and deafness was supported by two observations based on haplotype and mutation analysis of the kindred. First, a relative homozygous for the mutation was diagnosed at age 3 years with insulin-dependent diabetes mellitus, the central feature of Wolfram syndrome. Second, two relatives with normal hearing had an identical haplotype to that defining DFNA38, with the exception of the base pair at position 2146. Other rare variants of WFS1 co-inherited with deafness in the family could be excluded as disease-causing mutations on the basis of this hearing-associated haplotype. The possibility that 'mild' mutations in WFS1 might be a cause of non-syndromic deafness in the general population should be explored.

Structure of a BRCA1-BARD1 heterodimeric RING-RING complex

The RING domain of the breast and ovarian cancer tumor suppressor BRCA1 interacts with multiple cognate proteins, including the RING protein BARD1. Proper function of the BRCA1 RING domain is critical, as evidenced by the many cancer-predisposing mutations found within this domain. We present the solution structure of the heterodimer formed between the RING domains of BRCA1 and BARD1. Comparison with the RING homodimer of the V(D)J recombination-activating protein RAG1 reveals the structural diversity of complexes formed by interactions between different RING domains. The BRCA1-BARD1 structure provides a model for its ubiquitin ligase activity, illustrates how the BRCA1 RING domain can be involved in associations with multiple protein partners and provides a framework for understanding cancer-causing mutations at the molecular level.

BRCA1 and BRCA2 and the genetics of breast and ovarian cancer

Germline mutations in the tumor suppressor genes BRCA1 and BRCA2 predispose individuals to breast and ovarian cancers. Progress in determining the function of BRCA1 and BRCA2 suggests that they are involved in two fundamental cellular processes: DNA damage repair and transcriptional regulation. We evaluate current knowledge of BRCA1 and BRCA2 functions to explain why mutations in BRCA1 and BRCA2 lead specifically to breast and ovarian cancer. The BRCA1 and BRCA2 genes contain unusually high densities of repetitive elements. These features of the BRCAs genomic regions contribute to chromosomal instability of these genes. We propose that somatic alterations of BRCA1 and BRCA2 are common and driven by rearrangements between repetitive elements. Inherited and somatic mutations occur in BRCA1 and BRCA2; virtually all somatic mutations are the result of large genomic rearrangements. What are the consequences of such large somatic mutations of BRCA1 and BRCA2 in women with or without inherited mutations? The breast and ovary are estrogen-responsive tissues. Beginning in puberty, the breast epithelium proliferates rapidly in response to fluctuating levels of estrogen. We present a genetic model outlining how BRCA-deficient cells may gain uncontrolled proliferation leading to tumor formation. Central to this model of BRCA-mediated tumorigenesis are estrogen-mediated proliferation of breast and ovarian epithelium and the distinctive genomic context of the BRCA genes.

Identification of Id4 as a regulator of BRCA1 expression by using a ribozyme-library-based inverse genomics approach

Expression of the breast and ovarian cancer susceptibility gene BRCA1 is down-regulated in sporadic breast and ovarian cancer cases. Therefore, the identification of genes involved in the regulation of BRCA1 expression might lead to new insights into the pathogenesis and treatment of these tumors. In the present study, an "inverse genomics" approach based on a randomized ribozyme gene library was applied to identify cellular genes regulating BRCA1 expression. A ribozyme gene library with randomized target recognition sequences was introduced into human ovarian cancer-derived cells stably expressing a selectable marker [enhanced green fluorescence protein (EGFP)] under the control of the BRCA1 promoter. Cells in which BRCA1 expression was upregulated by particular ribozymes were selected through their concomitant increase in EGFP expression. The cellular target gene of one ribozyme was identified to be the dominant negative transcriptional regulator Id4. Modulation of Id4 expression resulted in inversely regulated expression of BRCA1. In addition, increase in Id4 expression was associated with the ability of cells to exhibit anchorage-independent growth, demonstrating the biological relevance of this gene. Our data suggest that Id4 is a crucial gene regulating BRCA1 expression and might therefore be important for the BRCA1 regulatory pathway involved in the pathogenesis of sporadic breast and ovarian cancer.

A novel sodium bicarbonate cotransporter-like gene in an ancient duplicated region: SLC4A9 at 5q31

BACKGROUND

Sodium bicarbonate cotransporter (NBC) genes encode proteins that execute coupled Na+ and HCO3- transport across epithelial cell membranes. We report the discovery, characterization, and genomic context of a novel human NBC-like gene, SLC4A9, on chromosome 5q31.

RESULTS

SLC4A9 was initially discovered by genomic sequence annotation and further characterized by sequencing of long-insert cDNA library clones. The predicted protein of 990 amino acids has 12 transmembrane domains and high sequence similarity to other NBCs. The 23-exon gene has 14 known mRNA isoforms. In three regions, mRNA sequence variation is generated by the inclusion or exclusion of portions of an exon. Noncoding SLC4A9 cDNAs were recovered multiple times from different libraries. The 3' untranslated region is fragmented into six alternatively spliced exons and contains expressed Alu, LINE and MER repeats. SLC4A9 has two alternative stop codons and six polyadenylation sites. Its expression is largely restricted to the kidney. In silico approaches were used to characterize two additional novel SLC4A genes and to place SLC4A9 within the context of multiple paralogous gene clusters containing members of the epidermal growth factor (EGF), ankyrin (ANK) and fibroblast growth factor (FGF) families. Seven human EGF-SLC4A-ANK-FGF clusters were found.

CONCLUSION

The novel sodium bicarbonate cotransporter-like gene SLC4A9 demonstrates abundant alternative mRNA processing. It belongs to a growing class of functionally diverse genes characterized by inefficient highly variable splicing. The evolutionary history of the EGF-SLC4A-ANK-FGF gene clusters involves multiple rounds of duplication, apparently followed by large insertions and deletions at paralogous loci and genome-wide gene shuffling.

Complex germline rearrangement of BRCA1 associated with breast and ovarian cancer

Germline mutations in BRCA1 predispose to breast and ovarian cancer. Most germline BRCA1 mutations are small insertions, deletions, or single base pair (bp) substitutions. These mutation classes are rarely found as somatic mutations in BRCA1. On the other hand, somatic deletions of multiple mega-base pairs (Mb) including BRCA1, as reflected by loss of heterozygosity, occur frequently in both inherited and sporadic breast and ovarian cancers. To determine whether deletions or rearrangements of hundreds to thousands of bps might contribute to inherited mutation in BRCA1, we developed a Long PCR strategy for screening the entire genomic BRCA1 locus in high-risk families. We evaluated genomic DNA from one high-risk family of European ancestry with BRCA1-linked cancer in which no genomic mutations had been detected using conventional methods. Long PCR revealed a complex mutation, g.12977 ins10 del1039 (based on GenBank L78833), comprising an inverted duplication and deletion in BRCA1 that removes portions of exon 3 and intron 3, including the 5' splice site for intron 3. As a result of the deletion, exon 3 is skipped, leading to a truncated protein and disease predisposition. Unlike previously reported large germline deletions in BRCA1, neither breakpoint resides within an Alu element. The g.12977 ins10 del1039 mutation was not detected among 11 other breast cancer families, nor among 406 breast cancer patients unselected for family history.

Complex germline rearrangement of BRCA1 associated with breast and ovarian cancer

Germline mutations in BRCA1 predispose to breast and ovarian cancer. Most germline BRCA1 mutations are small insertions, deletions, or single base pair (bp) substitutions. These mutation classes are rarely found as somatic mutations in BRCA1. On the other hand, somatic deletions of multiple mega-base pairs (Mb) including BRCA1, as reflected by loss of heterozygosity, occur frequently in both inherited and sporadic breast and ovarian cancers. To determine whether deletions or rearrangements of hundreds to thousands of bps might contribute to inherited mutation in BRCA1, we developed a Long PCR strategy for screening the entire genomic BRCA1 locus in high-risk families. We evaluated genomic DNA from one high-risk family of European ancestry with BRCA1-linked cancer in which no genomic mutations had been detected using conventional methods. Long PCR revealed a complex mutation, g.12977 ins10 del1039 (based on GenBank L78833), comprising an inverted duplication and deletion in BRCA1 that removes portions of exon 3 and intron 3, including the 5' splice site for intron 3. As a result of the deletion, exon 3 is skipped, leading to a truncated protein and disease predisposition. Unlike previously reported large germline deletions in BRCA1, neither breakpoint resides within an Alu element. The g.12977 ins10 del1039 mutation was not detected among 11 other breast cancer families, nor among 406 breast cancer patients unselected for family history.

Inheritance of the shared epitope and long-term outcomes of rheumatoid arthritis among community-based Caucasian females

Multiple HLA-DRB1 alleles encoding a shared epitope (SE) at amino acid positions 70-74 are associated with susceptibility and severity of rheumatoid arthritis (RA). We examined the relationship between the number and DRB1 genotype of SE alleles inherited and long-term outcomes of 180 community-based, Caucasian female RA patients followed annually for up to 12 years. Outcomes examined were physician assessment of RA course; annual measures of pain, function, and number of painful joint groups; history of joint surgery; and resource utilization. Models accounted for correlation among serial observations for the same patient and adjusted for patient age and disease stage. We examined two genetic models: a SE model in which patients were classified according to the number of SE copies inherited and a genotype model in which patients were categorized into one of six groups based on the inherited DRB1 genotype. We used likelihood ratio tests to compare these genetic models and to compare alternative model specifications. Our results demonstrate strong associations between inheritance of the SE and long-term outcomes of community-based Caucasian females with RA. However, the pattern of results is not consistent across the outcomes. An additive model of risk is apparent for history of joint surgery and RA hospitalization. In contrast, a near reversal of this pattern is apparent for function, joint pain, pain rating, and RA physician visits. Finally, although the genotype model did not appear to be a better predictive model for RA outcomes overall, it did reveal some striking heterogeneity of SE alleles that was masked by the more parsimonious SE model. For example, the odds ratio (OR) for joint surgery for patients with 2 SE copies (OR = 3.16) reflects an average of 2 very different ORs when patients are further categorized according to genotype groups 4 and 5 (OR = 1.3 and 11.9, respectively).

Relative predispositional effects and mode of inheritance of HLA-DRB1 alleles among community-based Caucasian females with rheumatoid arthritis

Multiple HLA-DRB1 alleles encoding a shared epitope (SE) at amino acid positions 70-74 are associated with susceptibility to rheumatoid arthritis (RA). However, the nature of the association and the mode of inheritance differ depending upon the source of RA patients and laboratory methodology. We studied the relative predispositional effects (RPE) and mode of inheritance of DRB1 alleles among a community-based sample of 180 RA patients and 116 healthy controls, all Caucasian females. Polymerase chain reaction (PCR)-based assays were used for DRB1 genotyping, and the genotypic distributions were analyzed by both the RPE and antigen genotype frequency among patients (AGFAP) methods. We examined the evidence of synergy among DRB1 alleles for RA risk by comparing the observed DRB1 genotype distribution to that predicted under Hardy-Weinberg equilibrium. Fifty-six percent of RA cases were attributable to DRB1 alleles encoding the SE. The RPEs of DRB1 alleles were *0401 > *0404 > *1001 > *0408 > *0101. The strength of the RA association was not significantly different for these alleles. The AGFAP analysis was consistent with a recessive mode of inheritance for DRB alleles, while an additive (dominant) model was rejected. We found no evidence of synergy for RA risk among individual DRB1 alleles based on comparison of the observed vs. predicted genotype distributions. These results suggest that among community-based Caucasian females with RA, the DRB1 RA susceptibility gene influences disease risk in a recessive fashion without synergy among individual DRB1 alleles.

Prevalence of founder BRCA1 and BRCA2 mutations among breast and ovarian cancer patients in Hungary

We have investigated the impact of BRCA1 and BRCA2 mutations that were frequently identified among Hungarian high-risk breast-ovarian cancer families (Ramus et al., 1997b, AJHG), on the development of breast and ovarian cancer in the general Hungarian population. The prevalence of 3 BRCA1 mutations (185delAG, 300T-->G and 5382insC) and 2 BRCA2 mutations (6174delT and 9326insA) was evaluated in a hospital-based consecutive series of 500 female breast cancer patients and 90 ovarian cancer patients, not selected for age at diagnosis or family history of cancer, as well as in 350 controls. Among breast cancer patients, 3.6% (18/500) carried a founder mutation: 9 BRCA1 300T-->G, 7 BRCA1 5382insC, 1 BRCA1 185delAG and 1 BRCA2 9326insA. Among ovarian cancer patients, 11% (10/90) carried a founder mutation: 5 BRCA1 185delAG, 4 BRCA1 300T-->G and 1 BRCA1 5382insC. One control carried a mutation, BRCA1 5382insC. Inherited breast cancer was more frequent among women with younger age at diagnosis: 6.1% of women younger than age 50 but 2.4% of women diagnosed at age 50 or older carried one of the founder mutations. There was no association between mutation status and age at diagnosis of ovarian cancer. Three of 23 medullary breast cancers were inherited (p = 0.038). Carrier status was also associated with a non-significant trend toward advanced tumor stage at diagnosis. These mutations could be evaluated among all ovarian cancer patients and breast cancer patients younger than age 60 and of Hungarian ancestry.

Evidence of a founder BRCA1 mutation in Scotland

BRCA1 mutations have been identified in breast and ovarian cancer families from diverse ethnic backgrounds. We studied 17 different families with the BRCA1 2800delAA mutation; seven were ascertained in Scotland (Dundee, Edinburgh, Glasgow, St Andrews), five in Canada (Toronto, Victoria) and five in the United States (Chicago, Philadelphia, Seattle). Overall there was a clear preponderance of Scottish ancestry. Genotype analysis performed on key members from 17 families was consistent with a common haplotype, strongly suggesting a single ancestral origin. A possible link was established between two families by tracing their genealogies through the records of the Registrar General for Scotland. This is the first example of a BRCA1 mutation likely to be derived from a common founder in Scotland. Further studies will be necessary to estimate more accurately the population frequency of the BRCA1 2800delAA mutation among unselected cases of breast and ovarian cancer in Scotland and the UK.

Insights into the functions of BRCA1 and BRCA2

Since BRCA1 and BRCA2 were cloned five years ago, unraveling their normal functions has posed fascinating problems for cancer biologists. Both genes are novel, and little of their normal function was revealed by their sequence. Both genes contribute to homologous recombination and DNA repair, to embryonic proliferation, to transcriptional regulation and, for BRCA1, to ubiquitination. But questions regarding BRCA1 and BRCA2 biology remain, and their resolution is critical for clinical development. Why do ubiquitously expressed genes that participate in universal pathways lead, when mutant, specifically to breast and ovarian cancer? Why are the same genes required for embryonic proliferation and for tumor suppression?

Hardy-Weinberg testing for HLA class II (DRB1, DQA1, DQB1, and DPB1) loci in 26 human ethnic groups

Testing the fit of population data to Hardy-Weinberg proportions is crucial in the validation of many current approaches in population genetic studies. In this paper, we tested fit to Hardy-Weinberg proportions using exact approaches for both the overall and individual heterozygote genotype data of four HLA Class II loci: DRB1, DQA1, DQB1, and DPB1, from 26 human populations. Eighty of 99 overall tests fit the Hardy-Weinberg expectation (73% for DRB1, 89% for DQA1, 81% for DQB1 and 81% for DPB1). Deviations from Hardy-Weinberg proportions were both locus and group specific. Although we could not rule out other mechanisms at work, the individual test results indicated that the departure was possibly partly due to recent admixture. Evidence for selection and other sources of deviation are also discussed.

Mutations in COL11A2 cause non-syndromic hearing loss (DFNA13)

We report that mutation of COL11A2 causes deafness previously mapped to the DFNA13 locus on chromosome 6p. We found two families (one American and one Dutch) with autosomal dominant, non-syndromic hearing loss to have mutations in COL11A2 that are predicted to affect the triple-helix domain of the collagen protein. In both families, deafness is non-progressive and predominantly affects middle frequencies. Mice with a targeted disruption of Col11a2 also were shown to have hearing loss. Electron microscopy of the tectorial membrane of these mice revealed loss of organization of the collagen fibrils. Our findings revealed a unique ultrastructural malformation of inner-ear architecture associated with non-syndromic hearing loss, and suggest that tectorial membrane abnormalities may be one aetiology of sensorineural hearing loss primarily affecting the mid-frequencies.

Single nucleotide polymorphisms (SNPs) in the estrogen receptor gene and breast cancer susceptibility

In order to evaluate the role of inherited variation in the estrogen receptor (ESR1) gene in human breast cancer, we determined intronic sequences flanking each ESRI exon; identified multiple SNPs and length polymorphisms in the ESR1 coding sequence, splice junctions and regulatory regions; and genotyped families at high risk of breast cancer and population-based breast cancer patients and controls. Of 10 polymorphic sites in ESR1, four are synonymous SNPs, two are nonsynonymous SNPs and four are length polymorphisms; five are novel. No ESR1 polymorphisms were associated with breast cancer, either in the high-risk families or the case-control study. We therefore conclude that inherited genetic variation is not a mechanism by which the estrogen receptor is commonly involved in breast cancer development.

Genomic views of human history

New tools of genomic analysis shed light on historical puzzles. Migrations of ancient peoples, differences in migration patterns of males and females, historical demography of cultures with ancient roots, and patterns of human genetic diversity are increasingly the focus of integrated analysis by historians, anthropologists, and geneticists.

BRCA1 and BRCA2 mutations in Ashkenazi Jewish families with breast and ovarian cancer

The strongest risk factors currently known for inherited predisposition to breast and ovarian cancer are mutations in BRCA1 and BRCA2. Two mutations in BRCA1 and one mutation in BRCA2 have been identified that are present to a particularly high degree in the Ashkenazi Jewish population due to ancient founder effects. To clarify the role of ancient and novel BRCA1 and BRCA2 mutations in the Ashkenazi Jewish population, families with a strong history of breast and ovarian cancer were examined. Seventeen Ashkenazi Jewish families with four or more breast or ovarian cancers were analyzed for ancient and novel mutations in BRCA1 and BRCA2. Ancient mutations existed in 9 families; 7 had the BRCA1 185 del AG mutation, 1 had BRCA1 5382 ins C, and 1 had BRCA2 6174 del T. A novel mutation, BRCA2 6425 del TT, was discovered in 1 of the remaining 8 families. Seven families with four or more cases of breast and ovarian cancer cannot be accounted for by either the ancient or novel mutations. Therefore, ancient mutations in BRCA1 and BRCA2 are present in approximately half of Ashkenazi Jewish families in this series, suggesting the possibility of novel mutations, either in BRCA1, BRCA2, or in currently unidentified gene(s), responsible for the remainder.

Inter- and intraindividual variation in Doppler ultrasonic indirect blood pressure measurements in healthy cats

This study was undertaken to evaluate reference ranges for systolic blood pressure (SBP) in cats under conditions mimicking a clinical setting. SBP was measured in 50 healthy adult cats of various ages (range, 1.5-16 years) and body weights (range, 2.2-6.1 kg) by Doppler ultrasonic sphygmomanometry. A cuff width of 2.5 cm was used, placed on the left antebrachium, and this represented a mean cuff width of 35% limb circumference (range, 31-42%). The mean (+/-SD) SBP in the 50 cats was 162 +/- 19 mm Hg (range 124-210), with only 1 cat having a SBP > or = 200 mm Hg. No significant difference (P > .05) in SBP was found between male and female cats, and no significant correlation was found between SBP and age (r(s) = 0.075) or body weight (r(s) = 0.007). Further studies in some of these cats indicated that allowing a period of 10 minutes for acclimatization to the environment where SBP was recorded resulted in a significant decrease in SBP from 176 +/- 17 to 157 +/- 21 mm Hg (n = 7) and that use of a 3.3-cm-width cuff resulted in a significant decrease in measured SBP from 168 +/- 13 to 164 +/- 13 mm Hg (n = 10). Reproducibility of SBP measurements was evaluated in 7 cats by assessing SBP 7 times at intervals of > or = 24 hours over a 10-day period. These 7 cats had a low intraindividual coefficient of variation of SBP measurements (CV < or = 7.9%) although 2 of the 7 cats had SBP values > 200 mm Hg on at least 1 occasion.

Tumor necrosis factor a microsatellite polymorphism is associated with rheumatoid arthritis severity through an interaction with the HLA-DRB1 shared epitope

OBJECTIVE

To determine whether tumor necrosis factor microsatellite a (TNFa) polymorphism is associated with severity of rheumatoid arthritis (RA), and to examine the evidence for interaction between TNFa and the HLA-DRB1 shared epitope (SE).

METHODS

One hundred seventy-one community-based white female RA patients were genotyped for both TNFa and HLA-DRB1 alleles. We performed pairwise association analyses, stratified analyses, and multivariate logistic regressions to determine whether TNFa was associated with 4 measures of RA severity, and whether there was significant interaction between TNFa and the HLA-DRB1 SE.

RESULTS

Simple pairwise analyses did not reveal significant association between TNFa polymorphism and RA severity. However, when the data were stratified by the presence versus absence of the SE, striking associations were observed between TNFa allele 11 (TNFa11) and RA severity. These analyses also demonstrated significant interaction between TNFa11 and the SE (P = 0.07-0.005), and this was confirmed in our multivariate regressions. Specifically, the most severe outcomes were observed among individuals who had inherited both TNFa11 and the SE (61-71% had severe RA based on 1 of the 4 outcomes). In contrast, individuals who had inherited TNFa11 in the absence of the SE had the best outcomes (8-21% with severe RA). The odds ratios comparing these 2 groups ranged from 8.8 to 22.7 for the 4 severity measures. The differential effect of TNFa11 according to the presence versus absence of the SE (and vice versa) illustrated their interaction with respect to RA severity.

CONCLUSION

The data suggest that TNFa is associated with RA severity through an interaction with the HLA-DRB1 SE.

Mapping the functional domains of BRCA1. Interaction of the ring finger domains of BRCA1 and BARD1

Breast cancer 1 (BRCA1) and BRCA1-associated RING domain 1 (BARD1) are multidomain proteins that interact in vivo via their N-terminal RING finger motif regions. To characterize functional aspects of the BRCA1/BARD1 interaction, we have defined the structural domains required for the interaction, as well as their oligomerization state, relative stability, and possible nucleic acid binding activity. We have found that the RING finger motifs do not themselves constitute stable structural domains but are instead part of larger domains comprising residues 1-109 of BRCA1 and residues 26-119 of BARD1. These domains exist as homodimers and preferentially form a stable heterodimer. Shorter BRCA1 RING finger constructs do not interact with BARD1 or with longer BRCA1 constructs, indicating that the heterodimeric and homodimer interactions are mediated by regions outside the canonical RING finger motif. Nucleic acid binding is a generally proposed function of RING finger domains. We show that neither the homodimers nor the heterodimer displays affinity for nucleic acids, indicating that the proposed roles of BRCA1 and BARD1 in DNA repair and/or transcriptional activation must be mediated either by other regions of the proteins or by additional cofactors.

Inherited breast cancer: an emerging picture

A role for BRCA1 and BRCA2 in the control of genome integrity easily fits a tumor suppressor model. It is well established that mutations in DNA repair genes lead to genomic instability (138). Genomic instability may directly lead to tumorigenesis by allowing for the accumulation of mutations in key cell cycle regulators (139). The studies summarized here suggest that BRCA1, BRCA2, RAD51. and BARD1 function as a biochemical complex. This complex apparently plays a role in one or more of the DNA damage response pathways. Experimental data suggest that BRCA1 and BRCA2 function as regulators of transcription. These observations highlight some of the fundamental questions that remain to be addressed in the study of the biology of these genes. Are the DNA repair and transcriptional regulatory functions of BRCA1 and BRCA2 related? BRCA1 and BRCA2 may maintain the integrity of the genome by regulating expression of genes directly involved in this process. Alternatively, if the functions are not related, which is required for suppression of tumorigenesis? Researchers also are grappling with another paradox. If BRCA1 and BRCA2 are ubiquitously expressed, why do mutations in BRCA1 and BRCA2 lead specifically to tumors primarily of the breast and ovary, as well as a limited number of other tissues to a lesser degree? Nothing to date has been revealed that would explain how alteration of the transcriptional regulatory function and or the DNA repair function ascribed to BRCA1 and BRCA2 would result in tumor specificity as both of these functions are essential to a broad spectrum of tissues. It is possible that BRCAI and BRCA2 may regulate genes expressed only in the breast and ovary. Similarly, there may be unidentified BRCA1 and BRCA2 co-factors that are active only in the breast and ovary and, therefore, are critical to tumorigenesis. All breast cancer is genetic, although only a small fraction of cases are attributable to inherited genetic predisposition. Most breast cancer is due to genetic alterations that are specific to breast epithelial cells, many of which remain unknown. Integration of genetic approaches into research designed to elucidate biological pathways of breast cancer tumorigenesis will ultimately lead to new information critical to the development of new tools for the diagnosis and treatment of disease.

Haplotype and phenotype analysis of nine recurrent BRCA2 mutations in 111 families: results of an international study

Several BRCA2 mutations are found to occur in geographically diverse breast and ovarian cancer families. To investigate both mutation origin and mutation-specific phenotypes due to BRCA2, we constructed a haplotype of 10 polymorphic short tandem-repeat (STR) markers flanking the BRCA2 locus, in a set of 111 breast or breast/ovarian cancer families selected for having one of nine recurrent BRCA2 mutations. Six of the individual mutations are estimated to have arisen 400-2,000 years ago. In particular, the 6174delT mutation, found in approximately 1% of individuals of Ashkenazi Jewish ancestry, was estimated to have arisen 29 generations ago (1-LOD support interval 22-38). This is substantially more recent than the estimated age of the BRCA1 185delAG mutation (46 generations), derived from our analogous study of BRCA1 mutations. In general, there was no evidence of multiple origins of identical BRCA2 mutations. Our study data were consistent with the previous report of a higher incidence of ovarian cancer in families with mutations in a 3.3-kb region of exon 11 (the ovarian cancer cluster region [OCCR]) (P=.10); but that higher incidence was not statistically significant. There was significant evidence that age at diagnosis of breast cancer varied by mutation (P<.001), although only 8% of the variance in age at diagnosis could be explained by the specific mutation, and there was no evidence of family-specific effects. When the age at diagnosis of the breast cancer cases was examined by OCCR, cases associated with mutations in the OCCR had a significantly older mean age at diagnosis than was seen in those outside this region (48 years vs. 42 years; P=.0005).

Cognitive failures and stress

138 healthy volunteers in four age groups completed the Cognitive Failures Questionnaire (Self and Other) as well as measures of attention, freedom from distractibility, daily stress, and trait-state anxiety. Self-reported and observed cognitive failures were strongly associated with stress and anxiety. Higher self-reported cognitive failure in one age group appeared tied to this finding. We discuss the usefulness of self-report of cognitive failures for neuropsychological practice.

Further characterization of the DFNA1 audiovestibular phenotype

BACKGROUND

Autosomal dominant, nonsyndromic, hereditary hearing impairment in a large Costa Rican kindred is caused by a mutation in the human homolog of the Drosophila diaphanous gene.

OBJECTIVE

To further characterize the phenotype of DFNA1 with comprehensive audiovestibular evaluation and computed tomography of the temporal bone.

PATIENTS

One affected child and 2 affected adults of the Costa Rican kindred who harbor a mutation in the diaphanous gene.

SETTING

Medical Center at the University of California, San Francisco.

INTERVENTION

Otologic and neuro-otologic examination; pure tone audiometry, speech audiometry, and immitance testing; auditory evoked potentials, electrocochleography, and otoacoustic emissions; electronystagmography and vestibular autorotation tests; and computed tomography of the temporal bone.

RESULTS

The youngest subject, an 8-year-old boy, had a mild hearing loss, intact stapedial reflexes, otoacoustic emissions at high frequencies, normal auditory evoked potentials, and electrocochleographic findings consistent with endolymphatic hydrops. The two adults had severe to profound bilateral sensorineural hearing impairment. Electronystagmography disclosed normal vestibular function. Computed tomography demonstrated normal external, middle, and inner ear structures.

CONCLUSIONS

These results suggest that the early low-frequency hearing loss in this family is associated with endolymphatic hydrops. Elucidation of the role of the diaphanous gene in hearing will therefore lead to a better understanding of the mechanism of endolymphatic hydrops.

The cancer-predisposing mutation C61G disrupts homodimer formation in the NH2-terminal BRCA1 RING finger domain

The breast and ovarian cancer tumor suppressor gene, BRCA1, encodes for a Zn2+-binding RING finger motif located near the protein NH2 terminus. The RING finger motif is characterized by eight conserved Cys and His residues which form two Zn2+-binding sites termed Site I and Site II. We used limited proteolysis in conjunction with matrix-assisted laser desorption ionization time-of-flight mass spectroscopy to investigate the metal binding properties and to probe the solution structures of wild-type and mutant BRCA1 constructs that include the RING finger. Our results show that the RING finger motif is part of a larger proteolysis-resistant structural domain which encompasses the first 110 residues of BRCA1. Analytical gel-filtration chromatography and chemical cross-linking experiments demonstrate that the BRCA1 NH2-terminal domain readily homodimerizes in solution. The cancer-predisposing C61G mutation, which alters a conserved Zn2+-binding residue, abolishes metal binding to Site II of the RING finger motif, while Site I remains intact and functional. The C61G mutation also results in increased proteolytic susceptibility of the COOH-terminal portion of the NH2-terminal domain and perturbs the oligomerization properties of BRCA1.

Frequency of breast cancer attributable to BRCA1 in a population-based series of American women

CONTEXT

Previous studies of BRCA1 mutation prevalence have been based on high-risk groups, yielding estimates that do not reflect the experience of the general population of US patients with breast cancer.

OBJECTIVE

To determine prevalence of known disease-related mutations and other variants in BRCA1 and how it differs by race, age at diagnosis, and family history status in a population-based sample of white and black patients with breast cancer unselected for family history.

DESIGN

Case-control study.

SETTING

A 24-county area of central and eastern North Carolina.

PARTICIPANTS

Cases were women aged 20 to 74 years diagnosed as having a first invasive breast cancer between May 1993 and June 1996. Controls were frequency matched to cases by 5-year age range and race. The first 211 cases and 188 controls regardless of race and the subsequent 99 cases and 108 controls of African American ancestry are included in this report.

MAIN OUTCOME MEASURE

Germline variants at any site in the coding sequence, splice junctions, 5' untranslated region, or 3' untranslated region of the BRCA1 gene were analyzed in cases, and selected variants were analyzed in controls. Screening was performed using multiplex single-strand conformation analysis, with all potential variants confirmed using genomic sequencing.

RESULTS

Three of 211 patients with breast cancer had disease-related variants at BRCA1, all of which were protein-truncating mutations. After adjustment for sampling probabilities, the proportion of patients with breast cancer with disease-related variants was 3.3% (95% confidence interval, 0%-7.2%) in white women and 0% in black women. Young age at diagnosis alone did not predict BRCA1 carrier status in this population. In white women, prevalence of inherited mutation was 23% for cases with family history of ovarian cancer, 13% for cases from families with at least 4 cases of breast cancer with or without ovarian cancer, and 33% for cases from families with both breast and ovarian cancer and at least 4 affected relatives. Because these results are based on few families at the highest levels of risk, confidence intervals around these estimates are wide. An additional 5 patients had rare missense mutations or a single amino acid deletion, the biological significance of which is unknown. In black women, a variant in the 3' untranslated region was statistically significantly more common in cases than in controls.

CONCLUSIONS

These data suggest that in the general US population, widespread screening of BRCA1 is not warranted. In contrast, BRCA1 mutations are sufficiently frequent in families with both breast and ovarian cancer, or at least 4 cases of breast cancer (at any age), that genotyping might be considered. The emerging picture of BRCA1 population genetics involves complex interactions of family history, age, and genetic ancestry, all of which should be taken into account when considering testing or interpreting results.

Mutation in transcription factor POU4F3 associated with inherited progressive hearing loss in humans

The molecular basis for autosomal dominant progressive nonsyndromic hearing loss in an Israeli Jewish family, Family H, has been determined. Linkage analysis placed this deafness locus, DFNA15, on chromosome 5q31. The human homolog of mouse Pou4f3, a member of the POU-domain family of transcription factors whose targeted inactivation causes profound deafness in mice, was physically mapped to the 25-centimorgan DFNA15-linked region. An 8-base pair deletion in the POU homeodomain of human POU4F3 was identified in Family H. A truncated protein presumably impairs high-affinity binding of this transcription factor in a dominant negative fashion, leading to progressive hearing loss.

SeqHelp: a program to analyze molecular sequences utilizing common computational resources

Here we describe a tool to analyze molecular sequences utilizing the internet and existing computational resources for molecular biology. The computer program SeqHelp organizes information from database searches, gene structure prediction, and other information to generate multiply aligned, hypertext-linked reports to allow for fast analysis of molecular sequences. The efficient and economical strategy in this program can be employed to study molecular sequences for gene cloning, mutation analysis, and identical sequence search projects.

Long terminal repeat and nef gene variants of human immunodeficiency virus type 1 in perinatally infected long-term survivors and rapid progressors

HIV-1 sequences from perinatally infected children were analyzed in the long terminal repeat (LTR) region and nef in order to investigate associations of viral variation and disease progression. Four long-term survivors who reached 10 years of age or older, and four rapid progressors who survived less than 2 years, participated in this study. LTR sequences of multiple independent viral variants from each individual were compared. No sequence pattern within the LTR consistently distinguished long-term survivors from rapid progressors or vice versa. Deletions and insertions within transcription factor binding sites of the LTR and nef ranging from 8 to 341 bp were found in viral variants from the eldest long-term survivor (LTS047). These deletions and duplications may be associated with the survival of LTS047 via an unknown mechanism. Among all children in this study, the sites in the untranslated region (NF-kappaB, SP1, and TATA box) were more conserved than the sites in the nef/LTR overlap region (NFAT, purine-rich region, USF, TCF1alpha), reflecting the importance of the sites in the untranslated region for viral replication. A mutation in the E box motif within the USF site among the sequences from a long-term survivor (LTS113) is predicted to disrupt protein binding and may be associated with slow disease progression. Mutations of the SP1-III site in a rapid progressor (RP056) indicate that this site is not necessary for rapid disease progression.

CCR5del32 in perinatal HIV-1 infection

CCR5, a chemokine receptor, serves as a coreceptor for macrophage-tropic HIV-1 (1-3). A 32-bp deletion within the gene encoding CCR5, CCR5del32, has been shown to prevent HIV-1 infection of T cells in the absence of a wild-type allele. This alteration is present in low frequency in Caucasian populations (4-6). To investigate the effect of CCR5del32 in perinatal HIV-1 transmission and disease progression, two cohorts of perinatally exposed infected and uninfected children were analyzed for the presence of the allele. Polymerase chain reaction (PCR) was used to identify CCR5del32 in prevalent and prospective cases among 144 African American children from New York City and 73 Caucasian children from Barcelona, Spain. HIV-1 transmission; clinical manifestations of disease, including encephalopathy, opportunistic infections, and death before 2 years of age; survival; Centers for Disease Control and Prevention (CDC) classification; and degree of immunosuppression were compared in children with and without CCR5del32. The allele frequency in HIV-1-infected African Americans (0.016) was lower than in Catalan children (0.041). No evidence for a dominant protective effect of CCR5del32 for HIV-1 transmission or disease progression was found in these cohorts.

Inherited mutations in PTEN that are associated with breast cancer, cowden disease, and juvenile polyposis

PTEN, a protein tyrosine phosphatase with homology to tensin, is a tumor-suppressor gene on chromosome 10q23. Somatic mutations in PTEN occur in multiple tumors, most markedly glioblastomas. Germ-line mutations in PTEN are responsible for Cowden disease (CD), a rare autosomal dominant multiple-hamartoma syndrome. PTEN was sequenced from constitutional DNA from 25 families. Germ-line PTEN mutations were detected in all of five families with both breast cancer and CD, in one family with juvenile polyposis syndrome, and in one of four families with breast and thyroid tumors. In this last case, signs of CD were subtle and were diagnosed only in the context of mutation analysis. PTEN mutations were not detected in 13 families at high risk of breast and/or ovarian cancer. No PTEN-coding-sequence polymorphisms were detected in 70 independent chromosomes. Seven PTEN germ-line mutations occurred, five nonsense and two missense mutations, in six of nine PTEN exons. The wild-type PTEN allele was lost from renal, uterine, breast, and thyroid tumors from a single patient. Loss of PTEN expression was an early event, reflected in loss of the wild-type allele in DNA from normal tissue adjacent to the breast and thyroid tumors. In RNA from normal tissues from three families, mutant transcripts appeared unstable. Germ-line PTEN mutations predispose to breast cancer in association with CD, although the signs of CD may be subtle.

Nonsyndromic deafness DFNA1 associated with mutation of a human homolog of the Drosophila gene diaphanous

The gene responsible for autosomal dominant, fully penetrant, nonsyndromic sensorineural progressive hearing loss in a large Costa Rican kindred was previously localized to chromosome 5q31 and named DFNA1. Deafness in the family is associated with a protein-truncating mutation in a human homolog of the Drosophila gene diaphanous. The truncation is caused by a single nucleotide substitution in a splice donor, leading to a four-base pair insertion in messenger RNA and a frameshift. The diaphanous protein is a profilin ligand and target of Rho that regulates polymerization of actin, the major component of the cytoskeleton of hair cells of the inner ear.