The publication of the human genome, more than a decade ago, alongside the development of high-throughput technologies for DNA sequencing, marked the dawn of a new era in genetics. Large genomic projects have been initiated to decipher the mysteries hidden within the human genetic code. With the rapidly ever-growing amount of genetic information, and the importance of understanding what it all means, there is a need to generate an interdisciplinary hub that will connect researchers, both experimentalists and bioinformaticians, along with physicians and community representatives in order to develop a common genomic language. This should lead to an accessible, readable and interpretive human genome with a short list of personal actionable items. We will then be able to declare that we are moving ever closer to the point at which one's own genome will affect one's personal life at a scope beyond our current comprehension.

As the demands of scientific research and application for specimens increase rapidly, biobanks in China have been springing up over the recent years. This paper summarizes Chinese biobanks through investigation and survey on operative, managerial, ethical conditions and challenges of biobanks. At present, hospitals and research institutes in China set up and operate most of the biobanks, collecting human specimens to support clinical and scientific research. With the development of bio-industry and arrival of the big data era, biobanks need not only collect and store human and non-human specimens but also to manage the big data associated with these specimens.

A lot has been written about the opportunities of the Internet for medicine, and lately, also for disease research specifically. Although it remains to be seen how significant and sustainable a change this will result in, some recent developments are highly relevant for the area of genetic research. User-friendly, low-threshold web-based tools do not only provide information to patients and other users, but they also supply user-generated data that can be utilized by both medical practice and medical research. Many of these developments have been below the radar of mainstream academic research so far. Issues related to data quality and standardization, as well as data protection and privacy, still need to be addressed. Dismissing these platforms as fads of a tiny privileged minority risks missing the opportunity to have our say in these debates.

Non-syndromic oral clefts comprising cleft lip with and without cleft palate (CL/P) and cleft palate only (CPO) are common birth defects worldwide. Their aetiology involves both environmental and genetic factors. FOXE1 has previously been reported to be associated with oral clefts in some populations. Here, we investigate whether mutations in FOXE1 play a part in the formation of oral cleft in a Thai population. We first performed PCR–RFLP to genotype a previously reported associated polymorphism, c.-1204C > G (rs111846096), in our cohort. No association was found. In addition, two unrelated unaffected controls were found to be homozygous GG, indicating that homozygous GG at this c.-1204 position was not sufficient for the development of oral clefts. We then sequenced the entire coding region of FOXE1 in 458 unrelated individuals (146 CPOs, 108 CL/Ps and 204 Thai controls). Five different non-synonymous variants, c.274G > T (p.D92Y), c.569C > G (p.P190R), c.569C > T (p.P190L), c.664C > T (p.R222C) and c.1090G > A (p.G364S), were identified in CPOs and one, c.572C > G (p.P191R), in CL/P. All these six variants were in heterozygous state, each identified in one patient, and absent in 204 controls. Except the p.P190R, which was previously reported, the other five variants were novel. Our study identifies probable susceptibility variants of FOXE1 for oral clefts in the Thai population.

A girl aged 6 presented with haematuria and her sister (aged 5) presented with haematuria and proteinuria. Family history showed multiple individuals suffering from end stage renal failure from the paternal side of the pedigree. Following kidney biopsy in the father and paternal grandmother, the pathological diagnosis was of focal segmental glomerulosclerosis (FSGS). Exome sequencing was undertaken in the proband's sister and grandmother. Genetic variants shared by both affected individuals were interrogated to identify the genetic cause of disease. Candidate variants were then sequenced in all the family members to determine segregation with the disease. A mutation of COL4A5 known to cause Alport syndrome segregated with disease from the paternal side of the pedigree and a variant in NPHS1 was present in both paediatric cases and inherited from their mother. This study highlights the advantages of exome sequencing over single gene testing; disease presentation can be heterogeneous with several genes representing plausible candidates; candidate gene(s) may be unavailable as a diagnostic test; consecutive, single gene testing typically concludes once a single causal mutation is identified. In this family, we were able to confirm a diagnosis of Alport syndrome, which will facilitate testing in other family members.

Familial isolated hyperparathyroidism (FIHP) can be encountered in the context of multiple endocrine neoplasia type 1 (MEN1), hyperparathyroidism and jaw tumour syndrome (HPT–JT) and in familial hypocalciuric hypercalcaemia (FHH). In these syndromes, germline mutations in the relevant genes (MEN1, HPRT2 and CaSR, respectively) are detected. In some FIHP cases, the causative gene is still elusive. The objective of this study is to define the genetic basis of FIHP in a Georgian Jewish family with FIHP using whole exome capture and sequencing. DNA extracted from two sibs and one offspring from a single family all affected with multiglandular hyperparathyroidism was subjected to whole exome capturing and sequencing using the Roche NimbleGen V2 chip and the Illumina HiSeq2000 sequencing platform. Genetic variants were detected and annotated using a combination of the Genome Analysis Tool Kit and in-house scripts. Subsequent confirmation of the mutations and co-segregation analyses were carried out by Sanger sequencing in additional affected and unaffected family members. Whole exome capture and sequencing revealed the collection of variations common to the three-sequenced patients, including a very rare previously described missense mutation (c.T1021C: p.W341R) in the MEN1 gene. The p.W341R mutation in the MEN1 gene showed complete co-segregation in the family. Whole exome capture and sequencing led to the discovery of a missense mutation in the MEN1 gene and ruling out of the additional candidates in a single experiment. The limited expressivity of this mutation may imply a specific genotype–phenotype correlation for this mutation.

The 9p21 chromosomal region has been associated with coronary artery disease (CAD) in many genome wide association studies (GWAS). To date no information exists regarding the rs1333039 SNP which showed the strongest association in the WTCCC GWAS with CAD risk in the Indian population. The present study attempts to replicate the findings in the Indian population.

Genotyping for rs1333049 was done in 229 cases and 151 controls by allele-specific real-time assay.

A higher frequency of the risk allele rs1333049C was seen in cases (0·60) as compared with controls (0·49), which associated with CAD risk both in univariate (OR = 1·564, 95%CI = 1·154–2·119, P = 0·003) and multivariate analysis (OR = 2·460, 95%CI = 1·139–5·314, P = 0·022). Increased frequency of the risk allele was seen in younger individuals with CAD where 40% individuals in the age group 30–55 years had the CC genotype as compared with 29 and 24·5% in the age group 56–65 years and > 65 years, respectively (CC versus GG, P = 0·045). Higher incidence of the CC genotype was seen in MI patients, but missed significance when compared with controls (OR = 1·361, 95%CI = 0·954–1·942, P = 0·084).

In conclusion, the rs1333049 variant is significantly associated with CAD risk and also with age of onset in the Western Indian population. However there are differences in the haplotype structure of this SNP with the neighbouring rs10757278 SNP, these differences emphasize the importance of genotyping all risk variants at this locus which could underlie the differences in risk susceptibility to CAD across populations.

With many molecular markers in many species, research efforts in quantitative genetics have focused on dissecting these traits and understanding the importance of factors such as correlated response due to hitchhiking or pleiotropy. Here, in an examination of long-term selection experiments in mice, the evidence strongly supports the primary importance of hitchhiking on the coat colour loci brown and dilute in mice selected for high weight gain. First, the amount of observed change in coat colour allele frequency could not be explained by genetic drift alone, implying that selection was of high importance. Second, the allele frequency changes included reversals in the direction change, but there were still positive correlations in the early generations with differences in weight gain between the phenotypes. Third, the correlation between the change in allele frequencies and phenotypic difference in weight gain declined over time, consistent with the decay expected from linkage associations. Fourth, the changes at both loci in a short-term selection experiment for low weight gain were in the opposite direction than the changes in the contemporaneous related population selected for high weight gain.

Calpain 10 (CAPN10) variants have been associated with the genetic susceptibility to type 2 diabetes (T2D). In the present case-control study, we analysed the distribution of SNP-19 insertion/deletion (I/D) polymorphism in a total of 607 samples (103 T2D cases and 102 healthy controls) from Brahmin; (100 T2D cases and 100 healthy controls) from Bania and (100 T2D cases and 102 healthy controls) from Jat Sikh ethnic groups of the North-West Indian population. Increased frequency of I allele and II genotype was found in T2D in Brahmin ethnic group [P = 0·003, OR = 2·83 (1·43–5·61 at 95% CI)]. Significant correlation between II genotype and body mass index (BMI) was also observed [P = 0·003, OR = 3·31 (1·52–7·20 at 95% CI)]. No association for the genotypes and alleles was seen in Banias and Jat Sikhs. Our data suggests that SNP-19 I/D variation in the CAPN10 gene is modulated by ethnicity and influences the susceptibility to T2D in the North-West Indian population. We also performed a meta-analysis of relevant studies to assess the validity of this association. Data from 13 case-control studies with 15 760 samples comprising of 8395 T2D cases and 7365 controls were finally analysed. Significant heterogeneity between individual studies was evident in dominant and codominant models. The results of present meta-analysis indicate an association of T2D with carriers of DD genotype of CAPN10 I/D polymorphism. However, further analyses on a larger sample size are required to establish a conclusive association in meta-analysis.

Several breast cancer risk prediction models have been validated in ethnically diverse populations, but none in Israeli high-risk women. To validate the accuracy of the IBIS and BOADICEA risk prediction models in Israeli high-risk women, the 10-year and lifetime risk for developing breast cancer were calculated using both BOADICEA and IBIS models for high-risk, cancer-free women, counselled at the Sheba Medical Center from 1 June 1996–31 May 2000. Women diagnosed with breast cancer by 31 May 2011 were identified from the Israeli National Cancer Registry. The observed to expected breast cancer ratios were calculated to evaluate the predictive value of both algorithms. Overall, 358 mostly (N = 205, 57·2%) Ashkenazi women, were eligible, age range at counselling was 20–75 years (mean 46·76 ± 9·8 years). Over 13·6 ± 1·45 years (range 11–16 years), 15 women (4·19%) were diagnosed with breast cancer, at a mean age of 57 ± 8·6 years. The 10-year risks assigned by BOADICEA and IBIS ranged from 0·2 to 12·6% and 0·89 to 21·7%, respectively. The observed:expected breast cancer ratio was 15/18·6 (0·8–95% CI 0·48–1·33) and 15/28·6 (0·52–95% CI 0·32–0·87), using both models, respectively. In Jewish Israeli high-risk women the BOADICEA model has a better predictive value and accuracy in determining 10-year breast cancer risk than the IBIS model.

Gene expression profiling using microarrays and xenograft transplants of human cancer cell lines are both popular tools to investigate human cancer. However, the undefined degree of cross hybridization between the mouse and human genomes hinders the use of microarrays to characterize gene expression of both the host and the cancer cell within the xenograft. Since an increasingly recognized aspect of cancer is the host response (or cancer–stroma interaction), we describe here a bioinformatic manipulation of the Affymetrix profiling that allows interrogation of the gene expression of both the mouse host and the human tumour. Evidence of microenvironmental regulation of epithelial mesenchymal transition of the tumour component in vivo is resolved against a background of mesenchymal gene expression. This tool could allow deeper insight to the mechanism of action of anti-cancer drugs, as typically novel drug efficacy is being tested in xenograft systems.

Autism spectrum disorders (ASDs) are lifelong neurodevelopmental disabilities that affect 1 in 88 children in the USA. Despite the high heritability, the genetic basis for a majority of the ASDs remains elusive. The considerable clinical and genetic heterogeneity pose a significant challenge technically. State-of-the-art high-throughput sequencing (HTS), which makes the analyses of any specific single/multiple genes or whole exomes feasible, has shown a promising perspective in disease gene discovery. To date, numerous genetic studies using HTS have been reported and many rare inherited or de novo mutations have been identified. This review will focus on the progress and prospective of genome studies of ASDs using HTS.

Compared with single markers, polygenic scores that evaluate the joint effects of multiple trait-associated variants are more effective in explaining the variance of traits and risk of diseases. In total, 182 CHDWB (Emory-Georgia Tech Center for Health Discovery and Well Being study) adults were genotyped to investigate the common variant contributions to three traits (height, BMI, serum triglycerides) and three diseases (coronary artery disease (CAD), type 2 diabetes (T2D) and asthma). Association was contrasted between weighted and simple allelic sum polygenic scores with quantitative traits, and with the Framingham risk scores for CAD and T2D. Although the cohort size is two or three orders of magnitude smaller than typical discovery cohorts, we were able to detect significant associations and to explain up to 5% of the traits by the genetic risk scores, despite a strong influence of outliers. An unexpected finding was that CAD-associated single nucleotide polymorphisms (SNPs) explain a significant amount of the variation for total serum cholesterol. Forward step-wise sequential addition of SNPs into the regression model showed that the top-ranked SNPs explain a large proportion of variance, whereas inclusion of gender and ethnicity also affect the performance of polygenic scores.

Edwards syndrome is the second most commonly seen trisomy. It was first described by John Hamilton Edwards in 1960. Although most cases result in termination or foetal loss, live births have been documented in 5%. Edwards syndrome is characterized by multisystem anomalies, of which holoprosencephaly (HPE) is observed in 4–8% of cases. The clinical findings correspond to the degree of HPE malformation. Convulsions and endocrinopathies are among the severe clinical findings. The most common endocrinopathies are central diabetes insipidus (DI), hypothyroidism, hypocortisolism and growth hormone deficiency. The coexistence of holoproencephaly and DI in Edwards syndrome was discussed under the light of literature.

A recent E-Rare workshop reviewed the ethical aspects of whole exome and whole genome-sequencing studies (WES and WGS, respectively) in rare diseases. Leveraging new genomic technologies, which output vast amounts of known and novel genetic variants, researchers are learning more about the genetic basis and mechanisms involved in rare diseases. In some cases, these findings are translated into diagnostic tools for the benefit of rare disease patients. Among the disclosed data, which can assist in treatment management, incidental findings await, bringing with them ethical concerns for the clinicians, researchers and patients.