BACKGROUND: On-going climate change will drastically modify agriculture in the future, with a need for more sustainable systems, in particular regarding animal production. In this context, genetic diversity is a key factor for adaptation to new conditions: local breeds likely harbor unique adaptive features and represent a key component of diversity to reach resilience. However, local breeds often suffer from small population sizes, which puts these valuable resources at risk of extinction. In chickens, population management programs were initiated a few decades ago in France, relying on a particular niche market that aims at promoting and protecting local breeds. We conducted a unique comprehensive study of 22 French local breeds, along with four commercial lines, to evaluate their genetic conservation status and the efficiency of the population management programs.
RESULTS: Using a 57K single nucleotide polymorphism (SNP) chip, we demonstrated that both the between- and within-breed genetic diversity levels are high in the French local chicken populations. Diversity is mainly structured according to the breeds\' selection and history. Nevertheless, we observed a prominent sub-structuring of breeds according to farmers\' practices in terms of exchange, leading to more or less isolated flocks. By analysing demographic parameters and molecular information, we showed that consistent management programs are efficient in conserving genetic diversity, since breeds that integrated such programs earlier had older inbreeding.
CONCLUSIONS: Management programs of French local chicken breeds have maintained their genetic diversity at a good level. We recommend that future programs sample as many individuals as possible, with emphasis on both males and females from the start, and focus on a quick and strong increase of population size while conserving as many families as possible. We also stress the usefulness of molecular tools to monitor small populations for which pedigrees are not always available. Finally, the breed appears to be an appropriate operational unit for the conservation of genetic diversity, even for local breeds, for which varieties, if present, could also be taken into account.

Aims: To explore new SNP sites of miRNAs associated with gastric cancer, thereby providing valuable biomarkers to diagnose and screen gastric cancer. Materials & methods: A 1:1 case-control study was carried out. Microarrays were used to screen the SNP loci of miRNAs in the genomes of matched pairs of patients, 96 with gastric cancer and 96 healthy controls. For validation, mass spectrometry was used to classify miRNA SNP loci in 622 pairs of subjects. Results: rs7143252 was linked to a higher occurrence of gastric cancer. Conclusion: These results suggest that rs7143252 could be used as a specific biomarker to diagnose and screen gastric cancer.

Sex-chromosome discordant chimerism (XX/XY chimerism) is a rare chromosomal disorder in humans. We report a boy with ambiguous genitalia and hypospadias, showing 46,XY[26]/46,XX[4] in peripheral blood cells. To clarify the mechanism of how this chimerism took place, we carried out whole-genome genotyping using a SNP array and microsatellite analysis. The B-allele frequency of the SNP array showed a mixture of three and five allele combinations, which excluded mosaicism but not chimerism, and suggested the fusion of two embryos or a shared parental haplotype between the two parental cells. All microsatellite markers showed a single maternal allele. From these results, we concluded that this XX/XY chimera is composed of two different paternal alleles and a single duplicated maternal genome. This XX/XY chimera likely arose from a diploid maternal cell that was formed via endoduplication of the maternal genome just before fertilization, being fertilized with both X and Y sperm.

BACKGROUND: In human genetic association studies with high-dimensional gene expression data, it has been well known that statistical selection methods utilizing prior biological network knowledge such as genetic pathways and signaling pathways can outperform other methods that ignore genetic network structures in terms of true positive selection. In recent epigenetic research on case-control association studies, relatively many statistical methods have been proposed to identify cancer-related CpG sites and their corresponding genes from high-dimensional DNA methylation array data. However, most of existing methods are not designed to utilize genetic network information although methylation levels between linked genes in the genetic networks tend to be highly correlated with each other.
RESULTS: We propose new approach that combines data dimension reduction techniques with network-based regularization to identify outcome-related genes for analysis of high-dimensional DNA methylation data. In simulation studies, we demonstrated that the proposed approach overwhelms other statistical methods that do not utilize genetic network information in terms of true positive selection. We also applied it to the 450K DNA methylation array data of the four breast invasive carcinoma cancer subtypes from The Cancer Genome Atlas (TCGA) project.
CONCLUSIONS: The proposed variable selection approach can utilize prior biological network information for analysis of high-dimensional DNA methylation array data. It first captures gene level signals from multiple CpG sites using data a dimension reduction technique and then performs network-based regularization based on biological network graph information. It can select potentially cancer-related genes and genetic pathways that were missed by the existing methods.

The aim of the current review is to report a-CGH abnormalities identified in fetuses with prenatally diagnosed fetal malformations in whom a normal karyotype was diagnosed with conventional cytogenetic analysis. A systematic electronic search of databases (PubMed/Medline, EMBASE/SCOPUS) has been conducted from inception to May, 2017. Bibliographic analysis has been performed according to PRISMA statement for review. The following keywords were used: \'array-CGH\' and \'fetal malformations\" and \"prenatal diagnosis\"; alternatively, \"microarray\", \"oligonucleotide array\", \"molecular biology\", \"antenatal diagnostics\", \"fetal diagnostics\", \"congenital malformations\" and \"ultrasound\" were used to capture both \"a-CGH\" and \"prenatal\". One-hundred and twelve fetuses with prenatally diagnosed fetal malformations with normal karyotyping and a-CGH abnormalities detected are described. Single or multiple microarray abnormalities diagnosed have been classified in relation to different organ/system affected. The most frequent a-CGH abnormalities were detected in cases of congenital heart diseases (CDHs), multiple malformations and central nervous system (CNS) malformations. Maternal or paternal carrier-state was seen in 19.64% (22/112), of cases while the number of reported de novo mutations accounted for 46.42% (52/112) of all CNVs microarray abnormalities. Array-comparative genomic hydridization (a-CGH) may become an integral and complemantary genetic testing when fetal malformations are detected prenatally in fetuses with normal cytogenetic karyotype. In addition, a-CGH enables the identification of CNVs and VOUS and improves the calculation of recurrent risk and the genetic counseling.

OBJECTIVE: To explore the candidate disease causing gene for a case with floppy infant syndrome (FIS).
METHODS: Single nucleotide polymorphism array (SNP array) was used for analyzing the whole genome copy number mutations in the proband. Multiple PCR combined with denaturing high performance liquid chromatography (DHPLC) was employed to verify the suspected mutations in the proband and his family members.
RESULTS: A large duplication arr [hg19] Xq13.1: 67 987 646-73 805 828, which spans approximately 5.818182 Mb and encompasses 66 known genes, was identified in the proband. The multiple PCR-DHPLC assay confirmed duplication of HDAC8, PHKA1, TAF1, DLG3, KIF4A, IGBP1, PJA1 and SLC16A2 genes in the proband. His mother and grandmother both had duplication of the above genes in one X chromosome, but his aunt had not.
CONCLUSIONS: The large Xq13.1 duplication identified by the SNP array probably underlies the FIS in this family. For its high-throughput, high resolution and capacity of automation, SNP array has provided a first line method for the genetic testing for infants featuring developmental delay with unknown reason, mental retardation, autism, multiple malformation and FIS.

OBJECTIVE: To explore the genetic basis for a couple with recurrent pregnancy loss by using single nucleotide polymorphism array (SNP array), chromosomal karyotype analysis, and fluorescence in situ hybridization (FISH).
METHODS: A SNP array was used for analyzing sample derived from the abortic tissue. The couple was analyzed with G-banded karyotyping and an Illumina Human CytoSNP-12 Beadchip assay. Based on the results, specific probes were designed to verify the chromosomal aberration by FISH.
RESULTS: The SNP array showed a 16.6 Mb duplication at 11q23.3-q25 and a 11 Mb deletion at 15q26.1-q26.3 in the abortic tissue. Combined with high-resolution G-banding analysis, the karyotype of the wife was verified to be 46,XX,t(11;15)(q24;q26.2). FISH analysis using probes for 11pter/11qter and 15qter confirmed that she has carried a balanced translocation, while the fetus has carried a derivative chromosome 15 derived from the maternal translocation.
CONCLUSIONS: SNP array can facilitate detection of balanced translocations which are difficult to be identified by conventional chromosomal karyotyping. The method does not necessitate cell culture and can well suit genetic analysis for couples with recurrent pregnancy loss.

High-throughput data generation platforms, like mass-spectrometry, microarrays, and second-generation sequencing are susceptible to batch effects due to run-to-run variation in reagents, equipment, protocols, or personnel. Currently, batch correction methods are not commonly applied to microbiome sequencing datasets. In this paper, we compare different batch-correction methods applied to microbiome case-control studies. We introduce a model-free normalization procedure where features (i.e. bacterial taxa) in case samples are converted to percentiles of the equivalent features in control samples within a study prior to pooling data across studies. We look at how this percentile-normalization method compares to traditional meta-analysis methods for combining independent p-values and to limma and ComBat, widely used batch-correction models developed for RNA microarray data. Overall, we show that percentile-normalization is a simple, non-parametric approach for correcting batch effects and improving sensitivity in case-control meta-analyses.

OBJECTIVE: To explore the clinical and genetic characteristics of a case with Pallister-Killian syndrome (PKS).
METHODS: Chromosomal karyotype of umbilical cord blood sample derived from a 36-year-old pregnant woman was analyzed by G-banding analysis. After birth, the child was further analyzed with single nucleotide polymorphism microarray (SNP array) and fluorescence in situ hybridization (FISH) using 12pter/12qter probes.
RESULTS: G-banding analysis showed that the fetus has a karyotype of 46,XY [77]/47,XY,+mar [23]. After birth, Affymetrix CytoScan 750K array analysis showed a segmental tetrasomy of arr [hg19] 12p13.33p11.1(173 786 - 34 835 641)×4 and a 34.6 Mb repeat at 12p13.33p11.1 with in the neonate. FISH analysis confirmed that 39% of cells harbored the 12p tetrasomy.
CONCLUSIONS: Combined clinical examination, G-banded chromosomal karyotyping, FISH and microarray analysis can delineate the origin and fragments of small supernumerary marker chromosomes and diagnose PKS with precision.

Caspases play a vital role during apoptosis. In addition to apoptosis, caspases play a role in cytokine gene induction and work to inhibit apoptosis. In order for individuals to thrive with useful tissue growth, the rate of cell growth and division must surpass the rate of cell division. It is well established that excessive cell death of embryonic cells is a vital process occurring before structural abnormalities, regardless of their nature. Here we describe a 13-month-old male patient with a 4.7Mb interstitial duplication of chromosome 2q33.1. This duplication was identified by chromosomal microarray (CMA) which is the first-tier clinical diagnostic test to identify copy number variants (CNVs) for patients with unexplained developmental delay or intellectual disability. This patient presents with global developmental delay, especially in speech, language, hypotonia, and bilateral simian creases. The duplicated region contains several disease-causing genes. We believe that the phenotype in this patient\'s case was likely related to the gain of caspase 8 and 10 genes.