RESUMEN
Preeclampsia is a serious complication of pregnancy, affecting both maternal and fetal health. In genome-wide association meta-analysis of European and Central Asian mothers, we identify sequence variants that associate with preeclampsia in the maternal genome at ZNF831/20q13 and FTO/16q12. These are previously established variants for blood pressure (BP) and the FTO variant has also been associated with body mass index (BMI). Further analysis of BP variants establishes that variants at MECOM/3q26, FGF5/4q21 and SH2B3/12q24 also associate with preeclampsia through the maternal genome. We further show that a polygenic risk score for hypertension associates with preeclampsia. However, comparison with gestational hypertension indicates that additional factors modify the risk of preeclampsia.
Asunto(s)
Predisposición Genética a la Enfermedad , Hipertensión Inducida en el Embarazo/genética , Herencia Multifactorial , Preeclampsia/genética , Proteínas Adaptadoras Transductoras de Señales/genética , Adulto , Anciano , Dioxigenasa FTO Dependiente de Alfa-Cetoglutarato/genética , Asia Central/epidemiología , Presión Sanguínea/genética , Estudios de Casos y Controles , Conjuntos de Datos como Asunto , Europa (Continente)/epidemiología , Femenino , Factor 5 de Crecimiento de Fibroblastos/genética , Sitios Genéticos/genética , Estudio de Asociación del Genoma Completo , Humanos , Hipertensión Inducida en el Embarazo/epidemiología , Proteína del Locus del Complejo MDS1 y EV11/genética , Persona de Mediana Edad , Preeclampsia/epidemiología , Embarazo , Estudios ProspectivosRESUMEN
Two familial forms of colorectal cancer (CRC), Lynch syndrome (LS) and familial adenomatous polyposis (FAP), are caused by rare mutations in DNA mismatch repair genes (MLH1, MSH2, MSH6, PMS2) and the genes APC and MUTYH, respectively. No information is available on the presence of high-risk CRC mutations in the Romanian population. We performed whole-genome sequencing of 61 Romanian CRC cases with a family history of cancer and/or early onset of disease, focusing the analysis on candidate variants in the LS and FAP genes. The frequencies of all candidate variants were assessed in a cohort of 688 CRC cases and 4567 controls. Immunohistochemical (IHC) staining for MLH1, MSH2, MSH6, and PMS2 was performed on tumour tissue. We identified 11 candidate variants in 11 cases; six variants in MLH1, one in MSH6, one in PMS2, and three in APC. Combining information on the predicted impact of the variants on the proteins, IHC results and previous reports, we found three novel pathogenic variants (MLH1:p.Lys84ThrfsTer4, MLH1:p.Ala586CysfsTer7, PMS2:p.Arg211ThrfsTer38), and two novel variants that are unlikely to be pathogenic. Also, we confirmed three previously published pathogenic LS variants and suggest to reclassify a previously reported variant of uncertain significance to pathogenic (MLH1:c.1559-1G>C).
Asunto(s)
Poliposis Adenomatosa del Colon/genética , Neoplasias Colorrectales Hereditarias sin Poliposis/genética , Reparación de la Incompatibilidad de ADN/genética , Predisposición Genética a la Enfermedad , Poliposis Adenomatosa del Colon/epidemiología , Poliposis Adenomatosa del Colon/patología , Adulto , Anciano , Neoplasias Colorrectales Hereditarias sin Poliposis/epidemiología , Neoplasias Colorrectales Hereditarias sin Poliposis/patología , ADN Glicosilasas/genética , Metilación de ADN/genética , Proteínas de Unión al ADN/genética , Femenino , Humanos , Masculino , Persona de Mediana Edad , Endonucleasa PMS2 de Reparación del Emparejamiento Incorrecto/genética , Homólogo 1 de la Proteína MutL/genética , Proteína 2 Homóloga a MutS/genética , Mutación , Factores de Riesgo , Rumanía/epidemiologíaRESUMEN
Background: Most pathogenic mutations in the BRCA2 gene carry a high risk of hereditary breast and ovarian cancer (HBOC). However, a stop-gain mutation, K3326* (rs11571833), confers risk of lung cancer and cancers of the upper-aero-digestive tract but only a modest risk of breast or ovarian cancer. The Icelandic population provides an opportunity for comprehensive characterization of the cancer risk profiles of K3326* and HBOC mutations because a single mutation, BRCA2 999del5, is responsible for almost all BRCA2-related HBOC in the population. Methods: Genotype information on 43 641 cancer patients and 370 971 control subjects from Iceland, the Netherlands, and the United States was used to assess the cancer risk profiles of K3326* and BRCA2 999del5. BRCA2 expression was assessed using RNAseq data from blood (n = 2233), as well as 52 tissues reported in the GTEx database. Results: The cancer risks associated with K3326* are fundamentally different from those associated with 999del5. We report for the first time an association between K3326* and small cell lung cancer (odds ratio [OR] = 2.06, 95% confidence interval [CI] = 1.35 to 3.16) and squamous cell carcinoma of the skin (OR = 1.69, 95% CI = 1.26 to 2.26). Individuals homozygous for K3326* reach old age and have children. Unlike BRCA2 999del5, the K3326* allele does not affect the level of BRCA2 transcripts, and the allele is expressed to the same extent as the wild-type allele. Conclusions: K3326* associates primarily with cancers that have strong environmental genotoxic risk factors. Expression of the K3326* allele suggests that a variant protein may be made that retains the DNA repair capabilities important to hormone-responsive tissues but may be less efficient in responding to genotoxic stress.
Asunto(s)
Carcinoma de Células Escamosas/genética , Genes BRCA2 , Predisposición Genética a la Enfermedad , Neoplasias Pulmonares/genética , Neoplasias Cutáneas/genética , Carcinoma Pulmonar de Células Pequeñas/genética , Alelos , Genotipo , Humanos , Islandia/epidemiología , Mutación , Países Bajos/epidemiología , Oportunidad Relativa , Polimorfismo de Nucleótido Simple , Estados Unidos/epidemiologíaRESUMEN
We performed a genome-wide association study of total hip replacements, based on variants identified through whole-genome sequencing, which included 4,657 Icelandic patients and 207,514 population controls. We discovered two rare signals that strongly associate with osteoarthritis total hip replacement: a missense variant, c.1141G>C (p.Asp369His), in the COMP gene (allelic frequency = 0.026%, P = 4.0 × 10-12, odds ratio (OR) = 16.7) and a frameshift mutation, rs532464664 (p.Val330Glyfs*106), in the CHADL gene that associates through a recessive mode of inheritance (homozygote frequency = 0.15%, P = 4.5 × 10-18, OR = 7.71). On average, c.1141G>C heterozygotes and individuals homozygous for rs532464664 had their hip replacement operation 13.5 years and 4.9 years earlier than others (P = 0.0020 and P = 0.0026), respectively. We show that the full-length CHADL transcript is expressed in cartilage. Furthermore, the premature stop codon introduced by the CHADL frameshift mutation results in nonsense-mediated decay of the mutant transcripts.
Asunto(s)
Proteína de la Matriz Oligomérica del Cartílago/genética , Proteínas de la Matriz Extracelular/genética , Predisposición Genética a la Enfermedad/genética , Genoma Humano/genética , Osteoartritis de la Cadera/genética , Análisis de Secuencia de ADN/métodos , Artroplastia de Reemplazo de Cadera , Células Cultivadas , Codón sin Sentido , Mutación del Sistema de Lectura , Expresión Génica , Frecuencia de los Genes , Estudio de Asociación del Genoma Completo , Genotipo , Humanos , Islandia , Estimación de Kaplan-Meier , Mutación Missense , Osteoartritis de la Cadera/cirugía , Polimorfismo de Nucleótido Simple , Reacción en Cadena de la Polimerasa de Transcriptasa Inversa , Factores de RiesgoRESUMEN
The great majority of thyroid cancers are of the non-medullary type. Here we report findings from a genome-wide association study of non-medullary thyroid cancer, including in total 3,001 patients and 287,550 controls from five study groups of European descent. Our results yield five novel loci (all with Pcombined<3 × 10-8): 1q42.2 (rs12129938 in PCNXL2), 3q26.2 (rs6793295 a missense mutation in LRCC34 near TERC), 5q22.1 (rs73227498 between NREP and EPB41L4A), 10q24.33 (rs7902587 near OBFC1), and two independently associated variants at 15q22.33 (rs2289261 and rs56062135; both in SMAD3). We also confirm recently published association results from a Chinese study of a variant on 5p15.33 (rs2736100 near the TERT gene) and present a stronger association result for a moderately correlated variant (rs10069690; OR=1.20, P=3.2 × 10-7) based on our study of individuals of European ancestry. In combination, these results raise several opportunities for future studies of the pathogenesis of thyroid cancer.
Asunto(s)
Carcinoma Papilar/genética , Sitios Genéticos , Estudio de Asociación del Genoma Completo , Neoplasias de la Tiroides/genética , Adulto , Pueblo Asiatico/genética , Estudios de Casos y Controles , Cromosomas Humanos/genética , Femenino , Regulación Neoplásica de la Expresión Génica , Frecuencia de los Genes/genética , Predisposición Genética a la Enfermedad , Variación Estructural del Genoma , Genotipo , Humanos , Masculino , Persona de Mediana Edad , Hormonas Hipofisarias/análisis , Factores de Riesgo , Cáncer Papilar Tiroideo , Glándula Tiroides/metabolismo , Neoplasias de la Tiroides/metabolismo , Población Blanca/genética , Secuenciación Completa del GenomaRESUMEN
AIMS: Atrial fibrillation (AF) is the most common sustained cardiac arrhythmia in man, causing substantial morbidity and mortality with a major worldwide public health impact. It is increasingly recognized as a highly heritable condition. This study aimed to determine genetic risk factors for early-onset AF. METHODS AND RESULTS: We sequenced the whole genomes of 8453 Icelanders and imputed genotypes of the 25.5 million sequence variants we discovered into 1799 Icelanders with early-onset AF (diagnosed before 60 years of age) and 337 453 controls. Each sequence variant was tested for association based on multiplicative and recessive inheritance models. We discovered a rare frameshift deletion in the myosin MYL4 gene (c.234delC) that associates with early-onset AF under a recessive mode of inheritance (allelic frequency = 0.58%). We found eight homozygous carriers of the mutation, all of whom had early-onset AF. Six of the homozygotes were diagnosed by the age of 30 and the remaining two in their 50s. Three of the homozygotes had received pacemaker implantations due to sick sinus syndrome, three had suffered an ischemic stroke, and one suffered sudden cardiac death. CONCLUSIONS: Through a population approach we found a loss of function mutation in the myosin gene MYL4 that, in the homozygous state, is completely penetrant for early-onset AF. The finding may provide novel mechanistic insight into the pathophysiology of this complex arrhythmia.
Asunto(s)
Fibrilación Atrial/genética , Mutación del Sistema de Lectura/genética , Cadenas Ligeras de Miosina/genética , Anciano , Fibrilación Atrial/etnología , Estudios de Casos y Controles , Muerte Súbita Cardíaca/etnología , Muerte Súbita Cardíaca/etiología , Femenino , Eliminación de Gen , Genes Recesivos/genética , Estudio de Asociación del Genoma Completo/métodos , Heterocigoto , Homocigoto , Humanos , Islandia/etnología , Masculino , Persona de Mediana Edad , Linaje , Factores de Riesgo , Sarcómeros , Alineación de Secuencia/métodos , Síndrome del Seno Enfermo/etnología , Síndrome del Seno Enfermo/genética , Accidente Cerebrovascular/etnología , Accidente Cerebrovascular/genéticaRESUMEN
Transcriptional and splicing anomalies have been observed in intron 8 of the CASP8 gene (encoding procaspase-8) in association with cutaneous basal-cell carcinoma (BCC) and linked to a germline SNP rs700635. Here, we show that the rs700635[C] allele, which is associated with increased risk of BCC and breast cancer, is protective against prostate cancer [odds ratio (OR) = 0.91, P = 1.0 × 10(-6)]. rs700635[C] is also associated with failures to correctly splice out CASP8 intron 8 in breast and prostate tumours and in corresponding normal tissues. Investigation of rs700635[C] carriers revealed that they have a human-specific short interspersed element-variable number of tandem repeat-Alu (SINE-VNTR-Alu), subfamily-E retrotransposon (SVA-E) inserted into CASP8 intron 8. The SVA-E shows evidence of prior activity, because it has transduced some CASP8 sequences during subsequent retrotransposition events. Whole-genome sequence (WGS) data were used to tag the SVA-E with a surrogate SNP rs1035142[T] (r(2) = 0.999), which showed associations with both the splicing anomalies (P = 6.5 × 10(-32)) and with protection against prostate cancer (OR = 0.91, P = 3.8 × 10(-7)).
Asunto(s)
Neoplasias de la Mama/genética , Carcinoma Basocelular/genética , Caspasa 8/genética , Neoplasias de la Próstata/genética , Empalme del ARN , Retroelementos , Neoplasias Cutáneas/genética , Adulto , Anciano , Anciano de 80 o más Años , Alelos , Secuencia de Bases , Neoplasias de la Mama/metabolismo , Neoplasias de la Mama/patología , Carcinoma Basocelular/metabolismo , Carcinoma Basocelular/patología , Caspasa 8/metabolismo , Femenino , Estudio de Asociación del Genoma Completo , Humanos , Intrones , Masculino , Persona de Mediana Edad , Datos de Secuencia Molecular , Oportunidad Relativa , Polimorfismo de Nucleótido Simple , Neoplasias de la Próstata/metabolismo , Neoplasias de la Próstata/patología , Neoplasias de la Próstata/prevención & control , Factores Protectores , Neoplasias Cutáneas/metabolismo , Neoplasias Cutáneas/patologíaRESUMEN
Gastric cancer is a serious health problem worldwide, with particularly high prevalence in eastern Asia. Genome-wide association studies (GWAS) in Asian populations have identified several loci that associate with gastric cancer risk. Here we report a GWAS of gastric cancer in a European population, using information on 2,500 population-based gastric cancer cases and 205,652 controls. We found a new gastric cancer association with loss-of-function mutations in ATM (gene test, P = 8.0 × 10(-12); odds ratio (OR) = 4.74). The combination of the loss-of-function variants p.Gln852*, p.Ser644* and p.Tyr103* (combined minor allele frequency (MAF) = 0.3%) also associates with pancreatic and prostate cancers (OR = 3.81 and 2.18, respectively) and gives an indication of risk of breast and colorectal cancers (OR = 1.82 and 1.97, respectively). Cancers in those carrying loss-of-function ATM mutations are diagnosed at a significantly earlier age than in non-carriers. Our results confirm an association between gastric cancer in Europeans and three loci previously reported in Asians, MUC1, PRKAA1 and PSCA, refine the association signal at PRKAA1 and support a pathogenic role for the tandem repeat identified in MUC1.
Asunto(s)
Proteínas de la Ataxia Telangiectasia Mutada/genética , Predisposición Genética a la Enfermedad/genética , Polimorfismo de Nucleótido Simple , Neoplasias Gástricas/genética , Anciano , Anciano de 80 o más Años , Algoritmos , Europa (Continente) , Femenino , Frecuencia de los Genes , Estudio de Asociación del Genoma Completo/métodos , Genotipo , Humanos , Modelos Logísticos , Masculino , Persona de Mediana Edad , Modelos Genéticos , Oportunidad Relativa , Factores de Riesgo , Análisis de Secuencia de ADN/métodosRESUMEN
In an ongoing screen for DNA sequence variants that confer risk of cutaneous basal cell carcinoma (BCC), we conduct a genome-wide association study (GWAS) of 24,988,228 SNPs and small indels detected through whole-genome sequencing of 2,636 Icelanders and imputed into 4,572 BCC patients and 266,358 controls. Here we show the discovery of four new BCC susceptibility loci: 2p24 MYCN (rs57244888[C], OR=0.76, P=4.7 × 10(-12)), 2q33 CASP8-ALS2CR12 (rs13014235[C], OR=1.15, P=1.5 × 10(-9)), 8q21 ZFHX4 (rs28727938[G], OR=0.70, P=3.5 × 10(-12)) and 10p14 GATA3 (rs73635312[A], OR=0.74, P=2.4 × 10(-16)). Fine mapping reveals that two variants correlated with rs73635312[A] occur in conserved binding sites for the GATA3 transcription factor. In addition, expression microarrays and RNA-seq show that rs13014235[C] and a related SNP rs700635[C] are associated with expression of CASP8 splice variants in which sequences from intron 8 are retained.
Asunto(s)
Carcinoma Basocelular/genética , Caspasa 8/genética , Factor de Transcripción GATA3/genética , Proteínas de Homeodominio/genética , Proteínas Nucleares/genética , Proteínas Oncogénicas/genética , Proteínas/genética , Neoplasias Cutáneas/genética , Factores de Transcripción/genética , Adolescente , Adulto , Anciano , Anciano de 80 o más Años , Estudios de Casos y Controles , Niño , Femenino , Predisposición Genética a la Enfermedad , Estudio de Asociación del Genoma Completo , Humanos , Islandia , Masculino , Proteínas de la Membrana , Persona de Mediana Edad , Proteína Proto-Oncogénica N-Myc , Población Blanca/genética , Adulto JovenRESUMEN
We conducted a search for rare, functional variants altering susceptibility to Alzheimer's disease that exploited knowledge of common variants associated with the same disease. We found that loss-of-function variants in ABCA7 confer risk of Alzheimer's disease in Icelanders (odds ratio (OR) = 2.12, P = 2.2 × 10(-13)) and discovered that the association replicated in study groups from Europe and the United States (combined OR = 2.03, P = 6.8 × 10(-15)).
Asunto(s)
Transportadoras de Casetes de Unión a ATP/genética , Enfermedad de Alzheimer/genética , Estudios de Casos y Controles , Estudios de Asociación Genética , Predisposición Genética a la Enfermedad , Haplotipos , Humanos , Mutación , Riesgo , Análisis de Secuencia de ADNRESUMEN
Here we describe the insights gained from sequencing the whole genomes of 2,636 Icelanders to a median depth of 20×. We found 20 million SNPs and 1.5 million insertions-deletions (indels). We describe the density and frequency spectra of sequence variants in relation to their functional annotation, gene position, pathway and conservation score. We demonstrate an excess of homozygosity and rare protein-coding variants in Iceland. We imputed these variants into 104,220 individuals down to a minor allele frequency of 0.1% and found a recessive frameshift mutation in MYL4 that causes early-onset atrial fibrillation, several mutations in ABCB4 that increase risk of liver diseases and an intronic variant in GNAS associating with increased thyroid-stimulating hormone levels when maternally inherited. These data provide a study design that can be used to determine how variation in the sequence of the human genome gives rise to human diversity.
Asunto(s)
Subfamilia B de Transportador de Casetes de Unión a ATP/genética , Subunidades alfa de la Proteína de Unión al GTP Gs/genética , Cadenas Ligeras de Miosina/genética , Anciano , Anciano de 80 o más Años , Fibrilación Atrial/genética , Parálisis Bulbar Progresiva/genética , Cromograninas , Femenino , Mutación del Sistema de Lectura , Frecuencia de los Genes , Predisposición Genética a la Enfermedad , Genoma Humano , Estudio de Asociación del Genoma Completo , Pérdida Auditiva Sensorineural/genética , Humanos , Mutación INDEL , Islandia , Hepatopatías/genética , Masculino , Persona de Mediana Edad , Anotación de Secuencia Molecular , Filogeografía , Polimorfismo de Nucleótido Simple , Receptores Acoplados a Proteínas G/genética , Riesgo , Análisis de Secuencia de ADN , Tirotropina/sangreRESUMEN
Genome-wide association studies (GWAS) of urinary bladder cancer (UBC) have yielded common variants at 12 loci that associate with risk of the disease. We report here the results of a GWAS of UBC including 1670 UBC cases and 90 180 controls, followed by replication analysis in additional 5266 UBC cases and 10 456 controls. We tested a dataset containing 34.2 million variants, generated by imputation based on whole-genome sequencing of 2230 Icelanders. Several correlated variants at 20p12, represented by rs62185668, show genome-wide significant association with UBC after combining discovery and replication results (OR = 1.19, P = 1.5 × 10(-11) for rs62185668-A, minor allele frequency = 23.6%). The variants are located in a non-coding region approximately 300 kb upstream from the JAG1 gene, an important component of the Notch signaling pathways that may be oncogenic or tumor suppressive in several forms of cancer. Our results add to the growing number of UBC risk variants discovered through GWAS.
Asunto(s)
Proteínas de Unión al Calcio/genética , Cromosomas Humanos Par 20/genética , Péptidos y Proteínas de Señalización Intercelular/genética , Proteínas de la Membrana/genética , Neoplasias de la Vejiga Urinaria/genética , Población Blanca/genética , Adulto , Anciano , Anciano de 80 o más Años , Estudios de Casos y Controles , Femenino , Predisposición Genética a la Enfermedad , Estudio de Asociación del Genoma Completo , Humanos , Proteína Jagged-1 , Masculino , Persona de Mediana Edad , Polimorfismo de Nucleótido Simple , Proteínas Serrate-JaggedRESUMEN
Through whole-genome sequencing of 2,630 Icelanders and imputation into 11,114 Icelandic cases and 267,140 controls followed by testing in Danish and Iranian samples, we discovered 4 previously unreported variants affecting risk of type 2 diabetes (T2D). A low-frequency (1.47%) variant in intron 1 of CCND2, rs76895963[G], reduces risk of T2D by half (odds ratio (OR) = 0.53, P = 5.0 × 10(-21)) and is correlated with increased CCND2 expression. Notably, this variant is also associated with both greater height and higher body mass index (1.17 cm per allele, P = 5.5 × 10(-12) and 0.56 kg/m(2) per allele, P = 6.5 × 10(-7), respectively). In addition, two missense variants in PAM, encoding p.Asp563Gly (frequency of 4.98%) and p.Ser539Trp (frequency of 0.65%), confer moderately higher risk of T2D (OR = 1.23, P = 3.9 × 10(-10) and OR = 1.47, P = 1.7 × 10(-5), respectively), and a rare (0.20%) frameshift variant in PDX1, encoding p.Gly218Alafs*12, associates with high risk of T2D (OR = 2.27, P = 7.3 × 10(-7)).
Asunto(s)
Amidina-Liasas/genética , Ciclina D2/genética , Diabetes Mellitus Tipo 2/genética , Variación Genética , Proteínas de Homeodominio/genética , Oxigenasas de Función Mixta/genética , Transactivadores/genética , Estatura/genética , Peso Corporal/genética , Estudios de Casos y Controles , Dinamarca , Diabetes Mellitus Tipo 2/patología , Femenino , Frecuencia de los Genes , Predisposición Genética a la Enfermedad , Estudio de Asociación del Genoma Completo , Humanos , Islandia , Irán , Masculino , Polimorfismo de Nucleótido Simple , Factores de RiesgoRESUMEN
To search for new sequence variants that confer risk of cutaneous basal cell carcinoma (BCC), we conducted a genome-wide association study of 38.5 million single nucleotide polymorphisms (SNPs) and small indels identified through whole-genome sequencing of 2230 Icelanders. We imputed genotypes for 4208 BCC patients and 109 408 controls using Illumina SNP chip typing data, carried out association tests and replicated the findings in independent population samples. We found new BCC susceptibility loci at TGM3 (rs214782[G], P = 5.5 × 10(-17), OR = 1.29) and RGS22 (rs7006527[C], P = 8.7 × 10(-13), OR = 0.77). TGM3 encodes transglutaminase type 3, which plays a key role in production of the cornified envelope during epidermal differentiation.
Asunto(s)
Antígenos de Superficie/genética , Carcinoma Basocelular/genética , Reguladores de Proteínas de Unión al GTP/genética , Variación Genética , Mutación de Línea Germinal , Transglutaminasas/genética , Adolescente , Adulto , Anciano , Anciano de 80 o más Años , Niño , Femenino , Predisposición Genética a la Enfermedad , Estudio de Asociación del Genoma Completo , Genotipo , Células Germinativas/metabolismo , Humanos , Masculino , Persona de Mediana Edad , Polimorfismo de Nucleótido Simple , Neoplasias Cutáneas/genética , Adulto JovenRESUMEN
BACKGROUND: Osteoporosis is a systemic skeletal disease characterised by reduced bone mineral density and increased susceptibility to fracture; these traits are highly heritable. Both common and rare copy number variants (CNVs) potentially affect the function of genes and may influence disease risk. AIM: To identify CNVs associated with osteoporotic bone fracture risk. METHOD: We performed a genome-wide CNV association study in 5178 individuals from a prospective cohort in the Netherlands, including 809 osteoporotic fracture cases, and performed in silico lookups and de novo genotyping to replicate in several independent studies. RESULTS: A rare (population prevalence 0.14%, 95% CI 0.03% to 0.24%) 210 kb deletion located on chromosome 6p25.1 was associated with the risk of fracture (OR 32.58, 95% CI 3.95 to 1488.89; p = 8.69 × 10(-5)). We performed an in silico meta-analysis in four studies with CNV microarray data and the association with fracture risk was replicated (OR 3.11, 95% CI 1.01 to 8.22; p = 0.02). The prevalence of this deletion showed geographic diversity, being absent in additional samples from Australia, Canada, Poland, Iceland, Denmark, and Sweden, but present in the Netherlands (0.34%), Spain (0.33%), USA (0.23%), England (0.15%), Scotland (0.10%), and Ireland (0.06%), with insufficient evidence for association with fracture risk. CONCLUSIONS: These results suggest that deletions in the 6p25.1 locus may predispose to higher risk of fracture in a subset of populations of European origin; larger and geographically restricted studies will be needed to confirm this regional association. This is a first step towards the evaluation of the role of rare CNVs in osteoporosis.
Asunto(s)
Cromosomas Humanos Par 6/genética , Osteoporosis/genética , Fracturas Osteoporóticas/genética , Estudios de Casos y Controles , Puntos de Rotura del Cromosoma , Estudios de Cohortes , Variaciones en el Número de Copia de ADN , Análisis Mutacional de ADN , Eliminación de Gen , Dosificación de Gen , Estudio de Asociación del Genoma Completo , Humanos , Cadenas de Markov , Persona de Mediana EdadRESUMEN
Renal cell carcinoma (RCC) represents between 80 and 90% of kidney cancers. Previous genome-wide association studies of RCC have identified five variants conferring risk of the disease. Here we report the results from a discovery RCC genome-wide association study and replication analysis, including a total of 2,411 patients and 71,497 controls. One variant, rs35252396[CG] located at 8q24.21, is significantly associated with RCC after combining discovery and replication results (OR=1.27, P(combined)=5.4 × 10(-11)) and has an average risk allele frequency in controls of 46%. rs35252396[CG] does not have any strongly correlated variants in the genome and is located within a region predicted to have regulatory functions in several cell lines, including six originating from the kidney. This is the first RCC variant reported at 8q24.21 and it is largely independent (r(2)≤0.02) of the numerous previously reported cancer risk variants at this locus.
Asunto(s)
Carcinoma de Células Renales/genética , Predisposición Genética a la Enfermedad , Neoplasias Renales/genética , Polimorfismo de Nucleótido Simple , Anciano , Carcinoma de Células Renales/epidemiología , Biología Computacional , Regulación Neoplásica de la Expresión Génica , Genoma Humano , Genotipo , Humanos , Islandia/epidemiología , Neoplasias Renales/epidemiología , Oportunidad Relativa , Factores de RiesgoRESUMEN
Low bone mineral density (BMD) is used as a parameter of osteoporosis. Genome-wide association studies of BMD have hitherto focused on BMD as a quantitative trait, yielding common variants of small effects that contribute to the population diversity in BMD. Here we use BMD as a dichotomous trait, searching for variants that may have a direct effect on the risk of pathologically low BMD rather than on the regulation of BMD in the healthy population. Through whole-genome sequencing of Icelandic individuals, we found a rare nonsense mutation within the leucine-rich-repeat-containing G-protein-coupled receptor 4 (LGR4) gene (c.376C>T) that is strongly associated with low BMD, and with osteoporotic fractures. This mutation leads to termination of LGR4 at position 126 and fully disrupts its function. The c.376C>T mutation is also associated with electrolyte imbalance, late onset of menarche and reduced testosterone levels, as well as an increased risk of squamous cell carcinoma of the skin and biliary tract cancer. Interestingly, the phenotype of carriers of the c.376C>T mutation overlaps that of Lgr4 mutant mice.
Asunto(s)
Neoplasias del Sistema Biliar/genética , Densidad Ósea/genética , Carcinoma de Células Escamosas/genética , Codón sin Sentido/genética , Fracturas Osteoporóticas/genética , Receptores Acoplados a Proteínas G/genética , Neoplasias Cutáneas/genética , Desequilibrio Hidroelectrolítico/genética , Animales , Australia , Dinamarca , Regulación hacia Abajo/genética , Femenino , Heterocigoto , Humanos , Islandia , Masculino , Menarquia/genética , Ratones , Ratones Noqueados , Fenotipo , Receptores Acoplados a Proteínas G/química , Receptores Acoplados a Proteínas G/deficiencia , Receptores Acoplados a Proteínas G/metabolismo , Testosterona/análisisRESUMEN
In Western countries, prostate cancer is the most prevalent cancer of men and one of the leading causes of cancer-related death in men. Several genome-wide association studies have yielded numerous common variants conferring risk of prostate cancer. Here, we analyzed 32.5 million variants discovered by whole-genome sequencing 1,795 Icelanders. We identified a new low-frequency variant at 8q24 associated with prostate cancer in European populations, rs188140481[A] (odds ratio (OR) = 2.90; P(combined) = 6.2 × 10(-34)), with an average risk allele frequency in controls of 0.54%. This variant is only very weakly correlated (r(2) ≤ 0.06) with previously reported risk variants at 8q24, and its association remains significant after adjustment for all known risk-associated variants. Carriers of rs188140481[A] were diagnosed with prostate cancer 1.26 years younger than non-carriers (P = 0.0059). We also report results for a previously described HOXB13 variant (rs138213197[T]), confirming it as a prostate cancer risk variant in populations from across Europe.
Asunto(s)
Adenocarcinoma/genética , Mutación , Neoplasias de la Próstata/genética , Anciano , Anciano de 80 o más Años , Secuencia de Bases , Línea Celular , Cromosomas Humanos Par 8 , Frecuencia de los Genes , Predisposición Genética a la Enfermedad , Genoma Humano , Estudio de Asociación del Genoma Completo , Proteínas de Homeodominio/genética , Humanos , Islandia , Masculino , Persona de Mediana Edad , Datos de Secuencia Molecular , Polimorfismo de Nucleótido Simple , Riesgo , Análisis de Secuencia de ADN , Población Blanca/genéticaRESUMEN
To search for sequence variants conferring risk of nonmedullary thyroid cancer, we focused our analysis on 22 SNPs with a P < 5 × 10(-8) in a genome-wide association study on levels of thyroid stimulating hormone (TSH) in 27,758 Icelanders. Of those, rs965513 has previously been shown to associate with thyroid cancer. The remaining 21 SNPs were genotyped in 561 Icelandic individuals with thyroid cancer (cases) and up to 40,013 controls. Variants suggestively associated with thyroid cancer (P < 0.05) were genotyped in an additional 595 non-Icelandic cases and 2,604 controls. After combining the results, three variants were shown to associate with thyroid cancer: rs966423 on 2q35 (OR = 1.34; P(combined) = 1.3 × 10(-9)), rs2439302 on 8p12 (OR = 1.36; P(combined) = 2.0 × 10(-9)) and rs116909374 on 14q13.3 (OR = 2.09; P(combined) = 4.6 × 10(-11)), a region previously reported to contain an uncorrelated variant conferring risk of thyroid cancer. A strong association (P = 9.1 × 10(-91)) was observed between rs2439302 on 8p12 and expression of NRG1, which encodes the signaling protein neuregulin 1, in blood.
