Genetic variants in novel pathways influence blood pressure and cardiovascular disease risk

Blood pressure (BP) is a heritable trait¹ influenced by multiple biological pathways and is responsive to environmental stimuli. Over one billion people worldwide have hypertension (BP ≥140 mm Hg systolic [SBP] or ≥90 mm Hg diastolic [DBP])². Even small increments in BP are associated with increased risk of cardiovascular events³. This genome-wide association study of SBP and DBP, which used a multi-stage design in 200,000 individuals of European descent, identified 16 novel loci: six of these loci contain genes previously known or suspected to regulate BP (GUCY1A3-GUCY1B3; NPR3-C5orf23; ADM; FURIN-FES; GOSR2; GNAS-EDN3); the other 10 provide new clues to BP physiology. A genetic risk score based on 29 genome-wide significant variants was associated with hypertension, left ventricular wall thickness, stroke, and coronary artery disease, but not kidney disease or kidney function. We also observed associations with BP in East Asian, South Asian, and African ancestry individuals. Our findings provide new insights into the genetics and biology of BP, and suggest novel potential therapeutic pathways for cardiovascular disease prevention.

Genome-wide association study identifies six new loci influencing pulse pressure and mean arterial pressure

Numerous genetic loci influence systolic blood pressure (SBP) and diastolic blood pressure (DBP) in Europeans ^1-3. We now report genome-wide association studies of pulse pressure (PP) and mean arterial pressure (MAP). In discovery (N=74,064) and follow-up studies (N=48,607), we identified at genome-wide significance (P= 2.7×10^-8 to P=2.3×10^-13) four novel PP loci (at 4q12 near CHIC2/PDGFRAI, 7q22.3 near PIK3CG, 8q24.12 in NOV, 11q24.3 near ADAMTS-8), two novel MAP loci (3p21.31 in MAP4, 10q25.3 near ADRB1) and one locus associated with both traits (2q24.3 near FIGN) which has recently been associated with SBP in east Asians. For three of the novel PP signals, the estimated effect for SBP was opposite to that for DBP, in contrast to the majority of common SBP- and DBP-associated variants which show concordant effects on both traits. These findings indicate novel genetic mechanisms underlying blood pressure variation, including pathways that may differentially influence SBP and DBP.

Contribution of TMC6 and TMC8 (EVER1 and EVER2) variants to cervical cancer susceptibility

Cervical cancer (CxCa) is caused by persistent human papillomavirus (HPV) infection; genetic predisposition is also suspected to play a role. Our study is a targeted candidate gene follow-up based on: (i) strong clinical evidence demonstrating that mutations in the TMC6 and TMC8 (EVER1 and EVER2) genes associate with the HPV-associated disease epidermodysplasia verruciformis (EV) and (ii) recent epidemiological data suggesting a genetic susceptibility conferred by polymorphisms in such genes for skin and CxCa. Clarifying the association of the TMC6/8 genes with risk of CxCa will help in understanding why some HPV-infected women develop persistent infection, cervical lesions and eventually cancer while others do not. Twenty-two single nucleotide polymorphisms (SNPs) harboring the TMC6/8 genes were genotyped in 2,989 cases with cervical intraepithelial neoplasia grade III or invasive CxCa and 2,281 controls from the Swedish population. Association was evaluated in logistic regression models. Two SNPs displayed association with cervical disease: rs2290907 [odds ratio (OR)(GGvsAA) = 0.6, 95% confidence interval (95% CI): 0.3-0.9, p = 0.02)] and rs16970849 (OR(AGvsGG) = 0.8, 95% CI: 0.66-0.98, p = 0.03). The present data support the involvement of the TMC6/8 region in CxCa susceptibility but further analyses are needed to replicate our findings, fully characterize the region and understand the function of the genetic variants involved.

Type-Specific Persistence of High-Risk Human Papillomavirus Infections in the New Independent States of the former Soviet Union Cohort Study

BACKGROUND

Prospective follow-up studies have recently suggested that persistent high-risk human papillomavirus (HPV) infections play a key role in the progression of CIN lesions and in the development of cervical cancer. However, data on type-specific persistence, viral integration, and the role of multiple infections are scanty.

MATERIALS AND METHODS

A cross-sectional/cohort study was conducted between 1998 and 2002 in three New Independent States of the former Soviet Union comprising a cohort of 3,187 women, of whom 854 women were followed up for a mean of 17 months (SD, 11.6). HPV genotyping was done with real-time PCR, detecting HPV types 16, 18/45, 31, 33/52/58, 35, and 39. The integration status of HPV16 was examined by using a novel Taqman-based PCR method.

RESULTS

The mean clearance time for the individual high- risk-type infection was 16.5 months (range = 0.9-34.9 months). HPV16 and HPV31 were the most persistent infections (clearance times = 18.1 and 16.2 months, respectively), whereas HPV39 infections cleared most rapidly. The mean copies per cell in HPV18/45, HPV31, HPV33/52/58, and HPV39 infections were higher in persisting HPV infections than in HPV infections that cleared, but the difference was not significant. Integration of HPV16 was not found to correlate with HPV persistence.

CONCLUSIONS

A large proportion of women remained high-risk HPV positive after 18 months. Coinfection with multiple HPV types, viral load, or integration status did not correlate with persistence of high-risk HPV infections.

Variants of chemokine receptor 2 and interleukin 4 receptor, but not interleukin 10 or Fas ligand, increase risk of cervical cancer

Cervical cancer is caused by persistent infection of oncogenic human papillomavirus (HPV). Most infected women clear the virus without developing cervical lesions and it is likely that immunological host factors affect susceptibility to cervical cancer. The impact of the human leukocyte antigen (HLA) locus on the risk of cervical cancer is established and several other genes involved in immunological pathways have been suggested as biologically plausible candidates. The aim of this study was to examine the potential role of polymorphisms in 4 candidate genes by analysis of 1,306 familial cervical cancer cases and 288 controls. The following genes and polymorphisms were studied: Chemokine receptor 2 (CCR-2) V64I; Interleukin 4 receptor alpha (IL-4R) I75V, S503P and Q576R; Interleukin 10 (IL-10) -592; and Fas ligand (FasL) -844. The CCR-2 64I variant was associated with decreased risk of cervical cancer; homozygote carriers of the 64I variant had an odds ratio of 0.31 (0.12-0.77). This association was detected in both carriers and noncarriers of the HLA DQB1*0602 cervical cancer risk allele. The IL-4R 75V variant was associated with increased risk of cervical tumors, cases homozygote for 75V had an odds ratio of 1.91 (1.27-2.86) with a tendency that the association was stronger in noncarriers of the DQB1*0602 allele. We did not find any association for IL-10 -592, or FasL -844, previously reported to be associated with cervical cancer in the Dutch and Chinese populations, respectively.

Prevalence of the most common high-risk HPV genotypes among women in three new independent states of the former Soviet Union

Type distribution of HPV has been studied in different geographic regions, but the data are scanty from the new independent states of the former Soviet Union. Here the HPV prevalence and distribution of the most frequent high-risk HPV types among 3,187 women at different risk for HPV and cervical intraepithelial neoplasia in Russia, Belarus, and Latvia is reported. HPV detection, type distribution and viral load analysis in DNA samples from cervical scrapes were done with real-time PCR-based assay detecting HPV types 16, 18, 31, 33, 35, 39, 45, 52, and 58. The overall HPV prevalence was 31.2%, HPV16 was the most prevalent type followed by HPV31 and HPV33 group. The overall HPV prevalences in Russia, Belarus and Latvia were 33.4%, 27.5%, and 26.2%. The type distributions were similar in these countries, except for Latvia where HPV39 was the third prevalent genotype. HPV prevalence was highest (40.8%) among women from sexually transmitted disease clinic, followed by 30.9% among gynecological outpatients and 27.2% in screening patients. HPV detection increased with cytological abnormality (P = 0.0001) and lesion grade in the biopsy (P = 0.0001), from 27% to 72% in normal samples to cancer, and from 64% to 77% in cervical intraepithelial neoplasia 1 to cancer. The normalized viral loads varied greatly between and among different HPV-types. The mean log HPV33 group copies/cell increased from negative for intraepithelial lesions to cancer (P = 0.049). Distribution of the most common high-risk HPV-types seems to be similar in these countries as reported in other major geographical regions.

Reduced incidence of cervical cancer in mothers of sons with allergic rhinoconjunctivitis, asthma or eczema

Because infection with human papillomavirus is a necessary cause of cervical cancer, it is likely that host immunological factors involved in defense against such infections are important for susceptibility to this cancer. By examining associations between allergy in sons and cervical cancer in their mothers, we aimed to test for genetic components involved in both allergy and cervical cancer development. Women born in Sweden between 1932 and 1960 with at least 1 son with medical records from military conscription examination were included in the study (N = 717,963). Among these women there were 41,910 in situ and 3,618 invasive cases of cervical cancer. Hazard ratios of in situ and invasive cervical cancer were estimated as functions of allergic rhinoconjunctivitis, asthma and eczema diagnoses in sons. Adjustment was made for the possible confounders: age, year of birth, education, socio-economic index, geography, number of conscripted sons and total number of offspring. The risk of in situ and invasive cervical cancer was lower for women having sons diagnosed with hypersensitivity (allergic rhinoconjunctivitis, asthma or eczema). Fully adjusted hazard ratios for women with 1 hypersensitive son were for in situ 0.86 (95% CI 0.84-0.88) and for invasive cervical cancer 0.82 (95% CI 0.74-0.91). The protective effects were similar between the 3 allergic diagnoses and increased with number of sons with a diagnosis. There was no significant association between non-cervical cancer in mothers and allergy in sons. These results strengthen the hypothesis that inherited immunological factors are important in determining risk of cervical cancer, probably by affecting mechanisms for viral persistence.

Identification of susceptibility loci for cervical carcinoma by genome scan of affected sib-pairs

Cervical cancer is caused by a combination of environmental and genetic risk factors. Infection by oncogenic types of human papillomavirus is recognized as the major environmental risk factor and epidemiological studies indicate that host genetic factors predispose to disease development. A number of genetic susceptibility factors have been proposed, but with exception of the human leukocyte antigen CHLA, class II, have not shown consistent results among studies. We have performed the first genomewide linkage scan using 278 affected sib-pairs to identify loci involved in susceptibility to cervical cancer. A two-step qualitative non-parametric linkage analysis using 387 microsatellites with an average spacing of 10.5 cM revealed excess allelic sharing at nine regions on eight chromosomes. These regions were further analysed with 125 markers to increase the map density to 1.28 cM. Nominal significant linkage was found for three of the nine loci [9q32 (maximum lod-score, MLS) =1.95, P<0.002), 12q24 (MLS=1.25, P<0.015) and 16q24 (MLS=1.35, P<0.012)]. These three regions have previously been connected to human cancers that share characteristics with cervical carcinoma, such as esophageal cancer and Hodgkin's lymphoma. A number of candidate genes involved in defence against viral infections, immune response and tumour suppression are found in these regions. One such gene is the thymic stromal co-transporter (TSCOT). Analyses of TSCOT single nucleotide polymorphisms further strengthen the linkage to this region (MLS=2.40, P<0.001). We propose that the 9q32 region contains susceptibility locus for cervical cancer and that TSCOT is a candidate gene potentially involved in the genetic predisposition to this disease.

Early integration of high copy HPV16 detectable in women with normal and low grade cervical cytology and histology

BACKGROUND

Integration of human papillomavirus (HPV) DNA has been considered a late event in cervical carcinogenesis. However, integrated forms of HPV were recently detected in cancer precursor lesions using a new real time polymerase chain reaction (PCR) to detect the deletions at the 3362-3443 region of HPV16 E2 OBJECTIVE: To study the frequency of HPV16 DNA integration in cervical lesions and compare the sensitivity of an additional upstream region of the E2 ORF (2962-3138) in detecting HPV integration.

METHODS

Using the TaqMan based PCR, HPV16 positive DNA samples were analysed in 164 cervical scrapings from women participating in a multicentre screening trial. Biopsy confirmation was available in 62 cases.

RESULTS

Primers targeting the 3362-3443 region detected the majority of E2 deletions. In only 23% of the samples was the E2 upstream region equal or better target than the 3362-3443 region. Mixed (episomal/integrated) pattern was the most prevalent physical state of HPV16, also present in PAP smears with normal morphology. Pure integrated form was most prevalent in HSIL and cancer lesions, but also detectable in low grade abnormalities (NSIL, ASC-US, LSIL). Women with only integrated HPV16 were almost 10 years older than those with episomal HPV16. Viral load of integrated HPV16 was related to cytological abnormality (p = 0.003) but not to histology.

CONCLUSIONS

Integrated HPV16 is present in low grade cervical lesions, mostly mixed with the episomal form. Women with the pure integrated form of HPV16 are older than those with the other forms.

Height at age 18 years is a strong predictor of attained education later in life: cohort study of over 950,000 Swedish men

BACKGROUND

Adult body height has been related to socioeconomic position in cross-sectional studies. Intelligence, shared family factors, and non-familial circumstances may contribute to associations between height and attained education, but their relative importance has been difficult to resolve.

METHODS

A nation-wide record-linkage cohort study of over 950 000 Swedish men born 1950-75 followed with respect to attained education for up to 27 years after measurement of height at age 18 (baseline). The association between height and attained education in later life was investigated by logistic regression modelling with adjustment for age, geography, parental socioeconomic position, and cognitive ability. Shared family factors were accounted for in analyses of full-brother-pairs using conditional logistic regression.

RESULTS

The odds ratio (OR) for attaining higher education 7-27 years after baseline was 1.10 [95% confidence interval (95% CI) 1.09-1.10] in fully adjusted models per 5 cm increase in height. Men taller than 194 cm were two to three times more likely to obtain a higher education as compared with men shorter than 165 cm. The association remained within brother-pairs, OR 1.08 (95% CI 1.07-1.10), suggesting that non-familial factors contribute to the association between height and education attainment. A significant interaction (P < 0.0001) was found between year of birth, height, and attained education, showing slightly weaker associations among later birth cohorts.

CONCLUSIONS

The strong positive association between height and educational achievement remaining after adjustment for year of birth, parental socioeconomic position, other shared family factors, and cognitive ability may reflect educational discrimination based on height although residual confounding cannot be ruled out.

Interaction of host and viral risk factors for development of cervical carcinoma in situ

Infection by oncogenic human papillomavirus (HPV) is a necessary but not sufficient cause of cervical carcinoma. Several host genetic and viral factors have been reported to increase the risk of carcinoma development given an HPV infection. In our study, we have analysed the contribution of HPV 16 E6 sequence subtype and allelic variation at human leukocyte antigen (HLA) class II loci to the risk of developing cervical carcinoma in situ. Non-European-like HPV 16 E6 sequence subtypes were not found to be associated with an increased risk of cervical carcinoma, as compared to European-like variants. However, an association was found between the HPV 16 E6 L83V variant and the DR*04-DQ*03 haplotype. This association has been observed in several independent studies and shows that both the host HLA class II genotype and viral subtype will affect the risk of an infection progressing into cervical carcinoma.

HLA class II allele control of HPV load in carcinomain situ of the cervix uteri

Human papillomavirus (HPV) infection is the most important risk factor for development of cervical carcinoma. Carriers of certain HLA class II alleles, e.g., DRB1*1501 and DQB1*0602, are more prone to HPV 16 infection and cervical carcinoma, whereas other alleles, e.g., DRB1*1301 and DQB1*0603, render carriers less susceptible to the disease. In our study comprising 484 cases and 601 controls, we examine the effect of HLA class II alleles on viral load of the oncogenic types HPV 18/45 and HPV 31 and risk of developing cervical carcinoma in situ. We find that carriers of the commonly reported protective DRB1*1301 and DQB1*0603 alleles have lower HPV 18/45 load compared to noncarriers and a lower risk of developing HPV 18/45-positive cervical carcinoma. This provides further evidence that the HLA class II-mediated immune response to HPV is important for controlling viral load and outcome of an infection.

A regulatory polymorphism in PDCD1 is associated with susceptibility to systemic lupus erythematosus in humans

Systemic lupus erythematosus (SLE, OMIM 152700) is a complex autoimmune disease that affects 0.05% of the Western population, predominantly women. A number of susceptibility loci for SLE have been suggested in different populations, but the nature of the susceptibility genes and mutations is yet to be identified. We previously reported a susceptibility locus (SLEB2) for Nordic multi-case families. Within this locus, the programmed cell death 1 gene (PDCD1, also called PD-1) was considered the strongest candidate for association with the disease. Here, we analyzed 2,510 individuals, including members of five independent sets of families as well as unrelated individuals affected with SLE, for single-nucleotide polymorphisms (SNPs) that we identified in PDCD1. We show that one intronic SNP in PDCD1 is associated with development of SLE in Europeans (found in 12% of affected individuals versus 5% of controls; P = 0.00001, r.r. (relative risk) = 2.6) and Mexicans (found in 7% of affected individuals versus 2% of controls; P = 0.0009, r.r. = 3.5). The associated allele of this SNP alters a binding site for the runt-related transcription factor 1 (RUNX1, also called AML1) located in an intronic enhancer, suggesting a mechanism through which it can contribute to the development of SLE in humans.

A regulatory polymorphism in PDCD1 is associated with susceptibility to systemic lupus erythematosus in humans

Systemic lupus erythematosus (SLE, OMIM 152700) is a complex autoimmune disease that affects 0.05% of the Western population, predominantly women. A number of susceptibility loci for SLE have been suggested in different populations, but the nature of the susceptibility genes and mutations is yet to be identified. We previously reported a susceptibility locus (SLEB2) for Nordic multi-case families. Within this locus, the programmed cell death 1 gene (PDCD1, also called PD-1) was considered the strongest candidate for association with the disease. Here, we analyzed 2,510 individuals, including members of five independent sets of families as well as unrelated individuals affected with SLE, for single-nucleotide polymorphisms (SNPs) that we identified in PDCD1. We show that one intronic SNP in PDCD1 is associated with development of SLE in Europeans (found in 12% of affected individuals versus 5% of controls; P = 0.00001, r.r. (relative risk) = 2.6) and Mexicans (found in 7% of affected individuals versus 2% of controls; P = 0.0009, r.r. = 3.5). The associated allele of this SNP alters a binding site for the runt-related transcription factor 1 (RUNX1, also called AML1) located in an intronic enhancer, suggesting a mechanism through which it can contribute to the development of SLE in humans.

Host genetic control of HPV 16 titer in carcinoma in situ of the cervix uteri

Cervical cancer is strongly associated with infection by oncogenic forms of human papillomavirus (HPV). Although most women are able to clear an HPV infection, some develop persistent infections that may lead to cancer. The determinants of persistent infection are largely unknown. We have previously shown that women developing carcinoma in situ of the cervix uteri have higher titers of HPV 16 long before development of cervical neoplasia, indicating that the immune response to HPV is important in determining the outcome of an infection. The HLA class II alleles DRB1*1501 and DQB1*0602 have previously been associated with an increased risk of HPV infection, and carriers of these alleles also tend to have more long-term infections. Together these results indicate that certain HLA alleles may affect the ability to control the HPV copy number. To evaluate this possibility, we studied the HLA class II DRB1*1501-DQB1*0602 haplotype, as well as the alleles individually, and the HPV 16 titer in 928 women from a retrospective case-control study (441 cases and 487 controls). Carriers of the haplotype DRB1*1501-DQB1*0602 allele have a significantly higher HPV 16 titer compared to noncarriers (t-test with unequal variance, p = 0.017). An association was found between the HLA haplotype carrier frequency and HPV 16 titer (Mantel-Haenszel statistics p = 0.005). To study whether titer is related to the persistency of infection, women were divided into groups with long-term and short-term infection. A strong correlation is seen between long-term infection and high viral load and between short-term infection and low viral load. These results show that host genetic factors, e.g., variation at the HLA class II loci studied, may affect the immune reaction to the virus and thereby indirectly increase the susceptibility to carcinoma in situ of the cervix uteri.

Susceptibility locus for epidermodysplasia verruciformis not linked to cervical cancer in situ

Cervical cancer is strongly associated with infection by oncogenic forms of human papillomavirus (HPV), mainly HPV 16 and HPV 18. The aim of this study was to test if a locus previously mapped to a region on chromosome 17 qter in patients with epidermodysplasia verucciformis (EV) and psoriasis and considered to be responsible for an increased susceptibility to HPV 5, also is linked to increased HPV susceptibility in cervical cancer in situ. We also wanted to test whether HPV 16 positivity cluster in families with cervical cancer. DNA was extracted from formalin fixed biopsies of 224 affected from 77 families diagnosed with cervical cancer in situ. Two microsatellite markers (D17S939 and D17S802) containing the locus were genotyped and linkage analysis was performed. No linkage was found to any of the two markers, neither when considering all cancer cases as affected nor when only considering HPV 16 infected cancer cases as affected in the analysis. We conclude that the susceptibility locus for HPV 5 infections associated with EV and psoriasis does not seem to affect susceptibility to HPV 16, frequently detected in cervical cancer. Also, positivity for HPV 16 did not show a significant clustering in families.

HLA class II alleles associated with infection by HPV16 in cervical cancer in situ

HLA class II alleles have been associated with an increased risk of developing cervical cancer through infection with oncogenic forms of human papilloma virus (HPV). We have examined the association of variation at the DRB1 and DQB1 loci with HPV16 infection and risk of development of cervical cancer by analysis of 440 cases diagnosed with cervical cancer in situ and 476 age-matched controls in a retrospective case-control study. The infection history of a woman was studied by analysis of cervical smears taken at multiple times during a period of up to 27 years (1969-95). The frequency of a number of alleles are either increased (DRB1*0801, DRB1*1501, DQB1*0402 and DQB1*0602) or decreased (DRB1*0101, DRB1*1301, DQB1*0501 and DQB1*0603) in the cancer patients compared to the controls. After correction for multiple testing, only the DQB1*0602 and the DRB1*1501 alleles remain associated with cancer and only in HPV16-infected patients (DQB1*0602: 102/264 (39%) vs. 130/476 (28%), p = 0.028 and DRB1*1501: 104/259 (40%) vs. 132/469 (28%), p = 0.027). These alleles are associated primarily with infection by HPV and only indirectly affect the risk of developing cervical cancer in situ. To study the impact of these alleles on persistence of infection, women with short-term infections were compared to those with long-term infections. Carriers of DQB1*0602 and DRB1*1501 were more frequent in the group with long-term HPV infections, indicating that these class II alleles contribute to the inability to clear an HPV infection.

Gastric cancer and human leukocyte antigen: distinct DQ and DR alleles are associated with development of gastric cancer and infection by Helicobacter pylori

DNA and sera from 130 cases of gastric cancer and 263 population-based controls were analyzed to study the association of HLA class II DR-DQ alleles with Helicobacter pylori (Hp) infection and the risk for gastric cancer. Presence of the DQA1*0102 allele was inversely and significantly associated with Hp seropositivity (P = 2 x 10(-5)), which is an independent replication of previous findings. However, this inverse relationship with Hp did not correspond with a reduced risk of gastric cancer. At the DRB1 locus, the *1601 allele was significantly associated with an increased gastric cancer risk with an odds ratio (95% confidence interval) of 8.7 (range, 2.7-28.0). The effect of *1601 was more pronounced among Hp-negative subjects, and the association was stronger with the diffuse, rather than with the intestinal, histological type of gastric cancer. Because none of the HLA alleles were associated with both Hp infection and gastric cancer, the HLA DR-DQ alleles are linked with gastric cancer risk through other mechanisms than an increased susceptibility to Hp infection.

Fine mapping of the SLEB2 locus involved in susceptibility to systemic lupus erythematosus

We have previously reported linkage of systemic lupus erythematosus to chromosome 2q37 in multicase families from Iceland and Sweden. This locus (SLEB2) was identified by linkage to the markers D2S125 and D2S140. In the present study we have analyzed additional microsatellite markers and SNPs covering a region of 30 cM around D2S125 in an extended set of Nordic families (Icelandic, Swedish, and Norwegian). Two-point linkage analysis in these families gave a maximum lod score at the position of markers D2S2585 and D2S2985 (Z = 4.51, PIC = 0.65), by applying a "model-free" pseudo-marker linkage analysis. Based on multipoint linkage analysis in the Nordic families, the most likely location of the SLEB2 locus is estimated to be in the interval between D2S125 and the position of markers D2S2585 and D2S2985, with a peak multipoint lod score of Z = 6.03, assuming a dominant pseudo-marker model. Linkage disequilibrium (LD) analysis was performed using the data from the multicase families and 89 single-case families of Swedish origin, using the same set of markers. The LD analysis showed evidence for association in the single-case and multicase families with locus GAAT3C11 (P < 0.0003), and weak evidence for association was obtained for several markers located telomeric to D2S125 in the multicase families. Thirteen Mexican families were analyzed separately and found not to have linkage to this region. Our results support the presence of the SLEB2 locus at 2q37.

Heritability of cervical tumours

Development of cervical cancer is strongly associated with genital infection of oncogenic types of human papillomavirus (HPV). However, the majority of women infected with HPV never develop cancer; thus, additional factors appear to be necessary. The relative importance of genetic and environmental factors to the development of cervical tumours is not known. Therefore, we have estimated the heritability of liability to this disease. The Swedish Cancer Register and the National Family Register were used to identify biological and adoptive mothers and full, half- and adoptive sisters of cases with cervical tumours, as well as age-matched controls. Tetrachoric correlations were calculated and model fitting techniques used to estimate the relative importance of shared genes and shared familial environment. Shared genes (heritability) explain 27% (95% CI 26%-29%) of the total variation in liability to the disease. A significant effect of shared familial environment was seen among sisters but not among mother/daughter relations. Sister-specific shared environment accounts for 2% (95% CI 1%-4%) of the variance. Our results indicate that development of cervical tumours depends, to a significant extent, on inherited genetic factors. Genetic predisposing factors may influence the likelihood of, sensitivity to or persistence of HPV infection, as well as the rate of tumour development.

Association analysis with microsatellite and SNP markers does not support the involvement of BCL-2 in systemic lupus erythematosus in Mexican and Swedish patients and their families

We have described suggestive linkage between microsatellite markers within the cytogenetic region 18q21-23 and SLE, a region where linkage with other autoimmune diseases has also been detected. The Bcl-2 gene located within this region, is a candidate gene because of its role in apoptosis, a physiological mechanism that could be deregulated in autoimmune disease. Furthermore, several studies have found abnormalities of Bcl-2 expression in SLE patients. We therefore sought to determine if the Bcl-2 gene is involved in SLE by studying members of a large cohort of Mexican SLE patients (n = 378) and 112 Swedish simplex families. Using a microsatellite marker and two single nucleotide polymorphisms located within the gene, we were unable to detect association between Bcl-2 and SLE in either population. We also tested whether combinations of alleles of the Bcl-2 and IL-10.G microsatellites would increase the risk for SLE. Our results do not support such hypothesis. Our findings suggest that linkage between SLE and the 18q21-23 region is due to a gene other than Bcl-2.

Viral load of human papilloma virus 16 as a determinant for development of cervical carcinoma in situ: a nested case-control study

BACKGROUND

Infection with certain types of human papillomavirus (HPV), which is common among young women, increases the risk of cervical cancer. However, less than 1% of young women positive for oncogenic types of HPV develop cervical cancer. We investigated whether the amount of HPV DNA is a useful predictor of progression to cervical carcinoma in situ.

METHODS

We estimated the amount of HPV 16 DNA by a PCR that uses the 5'-exonuclease (Taqman) method, in 478 women with cervical carcinoma in situ and 608 individually matched controls. To adjust for differences in the amount of genomic DNA between samples, we estimated the amount of a nuclear gene (beta-actin). We studied multiple smears (total 3835 archived samples) from each woman, taken over periods of up to 26 years, that covered normal cytology to development of cervical cancer.

FINDINGS

The risk of cervical carcinoma in situ increased with the amount of HPV 16 DNA. Analysis of the first smear from each woman, collected a mean of 7.8 years before cancer diagnosis, showed that women with the 20% highest amount of HPV 16 DNA were at a 60-fold higher risk of developing cervical carcinoma in situ than women negative for HPV 16. The first smear samples were classified as normal by squamous-cell cytology.

INTERPRETATION

Analysis of the amount of HPV DNA can predict cancer risk at a stage when current screening methods are uninformative. Testing for the amount of HPV 16 DNA during gynaecological health checks might strikingly improve our ability to distinguish between infections that have a high or low risk of progressing into cervical cancer.

Consistent high viral load of human papillomavirus 16 and risk of cervical carcinoma in situ: a nested case-control study

BACKGROUND

Persistent infection with certain types of human papillomavirus (HPV) is believed to be a prerequisite for the development of cervical neoplasia. Persistence may depend on certain characteristics, such as viral load, which has so far been given little attention. We investigated the association between HPV 16 viral load and cervical carcinoma in situ.

METHODS

We did a nested case-control study of women participating in cytological screening in Sweden. We used a sensitive quantitative PCR assay to estimate HPV 16 load in multiple smears for each woman, taken during a period of up to 26 years before diagnosis. We calculated C, values, which decrease as the number of viral DNA copies increases.

FINDINGS

2081 smears from 478 cases and 1754 smears from 608 controls were tested. Among cases, we found a consistently increased load of HPV 16 already 13 years or more before diagnosis, and when many smears were still cytologically normal. Women with high HPV 16 viral loads were at least 30 times the relative risk of HPV-16-negative women more than a decade before diagnosis. The increase in relative risk was constant over time. About 25% of women (95% CI 0.12-0.32) infected with a high viral load before age 25 years developed cervical carcinoma in situ within 15 years.

INTERPRETATION

Cervical carcinoma in situ associated with HPV 16 occurs mainly in HPV-16-positive women who have consistently high viral loads long term. Women at high risk could be identified by use of a quantitative HPV test in addition to cytological screening.

Cervical cancer risk: is there a genetic component?

Human papilloma virus (HPV) is a major risk factor for the development of cervical cancer. As only some infected women develop cancer, other factors must be important for disease development. Genetic epidemiological studies show that genetic factors contribute significantly to disease risk. Genetic susceptibility to HPV exposure and/or infection appears to be important in determining the individual risk to develop this virally induced cancer.

A susceptibility locus for human systemic lupus erythematosus (hSLE1) on chromosome 2q

To identify chromosomal regions containing susceptibility loci for systemic lupus erythematosus (SLE), we performed genome scans in families with multiple SLE patients from Iceland, a geographical and genetic isolate, and from Sweden. A number of chromosomal regions showed maximum lod scores (Z) indicating possible linkage to SLE in both the Icelandic and Swedish families. In the Icelandic families, five regions showed lod scores greater than 2.0, three of which (4p15-13, Z=3.20; 9p22, Z=2.27; 19q13, Z=2.06) are homologous to the murine regions containing the lmb2, sle2 and sle3 loci, respectively. The fourth region is located on 19p13 (D19S247, Z=2.58) and the fifth on 2q37 (D2S125, Z=2.06). Only two regions showed lod scores above 2.0 in the Swedish families: on chromosome 2q11 (D2S436, Z=2. 13) and 2q37 (D2S125, Z=2.18). The combination of both family sets gave a highly significant lod score at D2S125 of Z=4.24 in favor of linkage for 2q37. This region represents a new locus for SLE. Our results underscore the importance of studying well-defined populations for genetic analysis of complex diseases such as SLE.

Genetic analysis of the contribution of IL10 to systemic lupus erythematosus

OBJECTIVE

To study the contribution of the IL10 gene to the susceptibility to systemic lupus erythematosus (SLE).

METHODS

Analysis by fluorescent-semiautomated genotyping of a dinucleotide repeat located in the promoter region of the IL10 locus (microsatellite G).

RESULTS

No significant difference was found in the frequencies of the microsatellite alleles of 330 Mexican patients with SLE compared to 368 controls from the same population. Two-point linkage analyses were carried out using 13 Mexican, 13 Swedish, and 8 Icelandic families with 2 or more cases with SLE. No linkage was revealed between IL10 and SLE, using a variety of parameter settings.

CONCLUSION

Our results do not support that the IL10 gene contributes to the susceptibility to SLE in the populations we studied.

A comparison of genome-scans performed in multicase families with systemic lupus erythematosus from different population groups

Systemic lupus erythematosus is a disease of unknown etiology. Multiple genetic factors are believed to be involved in its pathogenesis. In addition, and due to genetic heterogeneity, these factors and/or their combinations may be different in different ethnic groups, while some might be shared between populations. We have performed genome scans in multicase families from three different population groups, two from Northern Europe, with a high degree of homogeneity, and the third from a recently admixed population of Mexican Mestizos. Although our family material is relatively small, the results presented here show that using family sets from well defined populations are sufficient to detect susceptibility loci for SLE. Our results also reveal the chromosomal regions most likely to contain susceptibility genes for SLE.

Analysis of intron sequences at the class II HLA-DRB1 locus: implications for the age of allelic diversity

Analyses of the coding sequences of HLA class II alleles have revealed high similarity between species, indicating that much of the polymorphism predates the separation of human (Homo) and chimpanzee (Pan), 4-7.4 million years ago. Recent studies of the intron sequences of alleles provide support for a much more recent origin and rapid generation of HLA alleles. At the DRB1 locus, intron analysis indicates that most of the allelic lineages have diverged from each other before the separation of Homo and Pan, consistent with the exon analysis. However, the intron sequences of alleles within lineages are almost identical, indicating that many of the alleles have been generated after the divergence of the Homo and Pan lineages.

HLA class II alleles in Amerindian populations: implications for the evolution of HLA polymorphism and the colonization of the Americas

The analysis of HLA allele frequencies in various Amerindian populations may shed light on the history of human migrations in the Americas; the overall reduction in the number of alleles relative to non-Amerindian populations and the observation that the same alleles and allelic lineages are "missing" in all Amerindian groups suggests an "Into America" population bottleneck. The identification of previously unreported (and presumably newly arisen) HLA-DRB1 alleles among isolated Amerindian groups, (DRB*0417 in Argentina, *08042 in Ecuador, DRB1*0807 in Brazil, and *0811 in Canada) suggests that these alleles may have been generated since the colonization of the Americas (about 20-30,000 years ago). These observations are difficult to reconcile with the notion, based on the analysis of exon-2 sequences, that most of the human DRB1 alleles are "ancient", that is, predate the divergence of the hominoids (4-7 myr). Recent analyses of DRB1 intron sequences, however, indicate that, although most of the allelic lineages are ancient, the alleles within a lineage (> 90% of the DRB1 alleles) have arisen relatively recently. For DRB1*0807, presumably generated by an Asp to Val change (GAT to GTT) at codon 57, strong selective pressures appear to be in operation, based on the high frequency (23%), and linkage disequilibrium patterns of this allele. The analysis of a complex microsatellite in the second intron in the Ticuna is consistent with the notion that the new Amerindian DR8 alleles arose from DRB1*0802, the only DR8 allele observed in most Amerindian populations.

Chromosome-specific panels of tri- and tetranucleotide microsatellite markers for multiplex fluorescent detection and automated genotyping: evaluation of their utility in pathology and forensics

A set of 391 microsatellite markers (Weber set 6), 85% of which consist of tri- and tetranucleotide repeat markers, were used to design chromosome-specific panels that allowed for a high degree of multiplexing with respect to the fragment size range and fluorophore (FAM, HEX, TET). This marker set has an average coverage of 10.5 cM, with the largest gap being 28.1 cM. The markers were divided into 49 panels, with a maximum degree of multiplexing of 15 markers per panel. The utility of the markers for analysis of DNA from blood, hair, and formalin-fixed archival tissue biopsies was evaluated with respect to amplification efficiency, product yield, and degree of preferential amplification of the shorter allele in heterozygotes. The amplification efficiency was inversely related to repeat length and amplicon length. Based on the analysis of DNA from formalin-fixed biopsies, 51 markers suitable for loss of heterozygosity (LOH) studies were identified. The utility of the marker set for genome scanning, LOH, and forensic analyses is discussed.

MHC class II haplotypes and linkage disequilibrium in primates

The loci encoding the major histocompatibility class II cell surface antigens DR, DQ, and DP exhibit a remarkable degree of allelic polymorphism. Strong linkage disequilibrium is also found between these loci in the human population. To study the evolutionary conservation of this disequilibrium the DQA1, DQB1, and DRB1-6 loci were analyzed in chimpanzee and gorilla by sequencing or/and oligonucleotide hybridization of PCR-amplified DNA. This analysis revealed several new DRB sequences. The distribution of DRB loci differs between human and nonhuman primate haplotypes, and the strong disequilibrium found on human haplotypes between alleles at DQA1 and DQB1 as well as between the DQ loci and the DRB1 locus was not detected in the nonhuman hominoids. Extensive recombination within and between the DR and DQ region appears to have occurred during the 3-7 million years since the divergence of the three species, resulting in little similarity of haplotypes between species. The strong disequilibrium found in the human species between these loci may either reflect haplotype-specific barriers to recombination, recent founder effects in the evolution of humans, or selection for specific haplotypes.

DNA typing of forensic material with mixed genotypes using allele-specific enzymatic amplification (polymerase chain reaction)

Biological material in forensic casework frequently contains a mixture of genotypes, with a predominance of material from the victim and only trace amounts from the person committing the crime. Physical separation of the two genotypes or preferential lysis of different cell types may sometimes be possible. However, it is often difficult to achieve complete separation due to the lysis of cells or lack of material. We have developed an enzymatic amplification system for the HLA DQA1 locus, that will allow the presence of individual alleles in a sample with mixed genotypes to be determined, independent of their initial proportion in the sample. This system permits the identification of an allele representing less than 10(-4) of the background genotype. Use of polymerase chain reaction (PCR) with general primers allows only alleles representing more than about 1% to be detected, while the allele-specific amplification represents up to a 1000-fold increase in sensitivity. This method was applied to a rape case and a combined rape and murder case; in both cases the biological evidential materials contained a mixture of alleles from the victim and the rapist. Allele-specific PCR revealed the presence of alleles identical to those of the suspect using DNA from a vaginal swab taken after a rape incident, whereas by using general primers in the PCR only trace amounts of alleles other than those of the victim were found. Similarly, allele-specific amplification of DNA from vaginal swabs from the murder case revealed the presence of alleles identical to those of the suspect, while standard PCR only indicated the presence of genetic material from the victim.

Shared epitopes among HLA class II alleles: gene conversion, common ancestry and balancing selection

The extent and pattern of HLA class II sequence polymorphism raise a variety of evolutionary questions, notably those concerning the genetic mechanisms for generating diversity, the rate of change and the nature of the selection pressure maintaining this variation. Phylogenetic analysis of primate MHC class II sequences suggests that the allelic lineages are ancient, having diverged long before separation of the hominoid species. For the beta-chain loci, however, considerable allelic diversification within these lineages has occurred after speciation. The striking patchwork pattern of polymorphism with different alleles containing common sequence motifs can be accounted for by common ancestry, by gene conversion or by convergent evolution, depending on the location of the shared epitope.

Allelic diversity is generated by intraexon sequence exchange at the DRB1 locus of primates

The loci encoding the class II cell surface antigens HLA-DR, -DQ, and -DP exhibit a remarkable degree of allelic polymorphism. Most of the class II allelic diversity is localized to the second exon, which encodes a beta-pleated sheet followed by an alpha-helical domain. Here, phylogenetic analysis of 39 human DRB1 alleles and 21 DRB1 alleles obtained by polymerase chain reaction (PCR) amplification from a set of closely related primates reveals that sequences encoding the beta-pleated sheet and those encoding the alpha-helix of the second domain have different evolutionary histories. The polymorphisms in the beta-pleated sheet have been conserved between species and appear to reflect the ancestral relationships among haplotypes, whereas polymorphic segments encoding the alpha-helical domain appear to have been inserted by interallelic sequence exchange into the framework of different ancestral DRB1 sequences. Allelic polymorphism at the DRB1 locus may thus have been generated in part by combining different variants of the two structural domains.

The evolution of allelic diversity at the primate major histocompatibility complex class II loci

The evolutionary history of polymorphism at the DQ alpha, DQ beta, and DR beta loci appears to be quite distinct and reflects different genetic mechanisms and selection pressures for the different loci. Phylogenetic analysis of sequences from a variety of species allows the tentative reconstruction of the order of gene duplication and of allelic diversification. Some of the major allelic types or lineages appear to be very old (greater than 20 myr) and selection has acted to maintain these ancient allelic types as well as, in the case of the DR beta loci, to favor new variants generated by recombining beta-sheet and alpha-helix domains. Phylogenetic analysis can also reveal balancing selection at individual residues of the class II beta chains. The highest number of phylogenetically inferred changes attributed to balancing selection was found at beta-chain residues located in the ABS and at those residues implicated in disease susceptibility. For some residues, the number of different amino acids observed at individual polymorphic positions is highly restricted and the few tolerated residues are common to all primate species studied. This observation supports the view that these positions are subject to some form of balancing selection.

Allelic diversification at the class II DQB locus of the mammalian major histocompatibility complex

The allelic diversity at HLA class II loci either arose after the divergence of hominoid lineages or, alternatively, the polymorphism was present before speciation and has been maintained by selection. Here, we report the use of oligonucleotide primers to amplify, by the polymerase chain reaction, and sequence the polymorphic second exon of the DQB locus from 11 species, spanning more than 40 million years of mammalian evolution. Phylogenetic analysis reveals that of the four human DQB allelic types (DQB1-B4), three (DQB1-3) were found in chimpanzee and gorilla and two (DQB3 and -4) were identified in the rhesus monkey, suggesting that some of these types are 5-20 million years old. The ratio of replacement to silent substitutions was calculated between members of the same allelic type from different species. These results suggest that the evolution of the DQB3 allelic type is more constrained than that of the DQB1 allelic type; both evolve more slowly than the DXB locus, a linked but presumably nonexpressed locus. Further, the clustering of allelic subtypes by species in the phylogenetic tree indicates that allelic diversification has occurred subsequent to the divergence of hominoids. Finally, some haplotype combinations of DQA and DQB alleles are common to several hominoid species and may have been maintained for at least 5 million years.

No evidence for illegitimate young in monogamous and polygynous warblers

In animals with internal fertilization, paternity is uncertain. In birds, the occurrence of copulations outside the pair-bond has been documented in a number of species, but the extent to which these result in illegitimate young is largely unknown, and constitutes a major deficiency in our understanding of avian mating systems. The analysis of tandemly repeated sequences (minisatellites), has enhanced our ability to make individual identifications and paternity determinations. Here we describe the use of a bird minisatellite DNA probe in assigning paternity in natural populations of the monogamous willow warbler Phylloscopus trochilus and of the polygynous wood warbler Phylloscopus sibilatrix. In both species this probe detects a multiple locus pattern and a single locus that exhibits a variable number of tandem repeats. Although we observed intrusions by non-resident males into the territories of paired males and extra-pair copulations, no illegitimate offspring were detected among 176 young from 32 families of both species, implying that extra-pair copulations have little or no genetic impact.

Ancient roots for polymorphism at the HLA-DQ alpha locus in primates

The genes encoding the human histocompatibility antigens (HLA) exhibit a remarkable degree of polymorphism as revealed by immunologic and molecular analyses. This extensive sequence polymorphism either may have been generated during the lifetime of the human species or could have arisen before speciation and been maintained in the contemporary human population by selection or, possibly, by genetic drift. These two hypotheses were examined using the polymerase chain reaction method to amplify polymorphic sequences from the DQ alpha locus, as well as the DX alpha locus, an homologous but nonexpressed locus, in a series of primates that diverged at known times. In general, the amino acid sequence of a specific human DQ alpha allelic type is more closely related to its chimpanzee or gorilla counterpart than to other human DQ alpha alleles. Phylogenetic analysis of the silent nucleotide position changes shows that the similarity of allelic types between species is due to common ancestry rather than convergent evolution. Thus, most of the polymorphism at the DQ alpha locus in the human species was already present at least 5 million years ago in the ancestral species that gave rise to the chimpanzee, gorilla, and human lineages. However, one of the DQ alpha alleles may have arisen after speciation by recombination between two ancestral alleles.

PCR and DNA sequencing

Specific DNA segments defined by the sequence of two oligonucleotides can be enzymatically amplified up to a millionfold using the polymerase chain reaction (PCR). One of the most significant uses of this technique is for generation of sequencing templates, either from cloned inserts or directly from genomic DNA. To avoid the problem of reassociation of the linear DNA strands in the sequencing reaction, ssDNA templates can be produced directly in the PCR or generated directly from dsDNA by enzymatic treatment, electrophoretic separation or affinity purification. By combining PCR with direct sequencing, both the amplification and the sequencing reaction can be performed in the same vial. Finally, use of fluorescently labeled terminators or sequencing primers will allow the whole procedure to be amenable to complete automation.