@article {882, title = {dbMTS: A comprehensive database of putative human microRNA target site SNVs and their functional predictions.}, journal = {Hum Mutat}, volume = {41}, year = {2020}, month = {2020 06}, pages = {1123-1130}, abstract = {

MicroRNAs (miRNA) are short noncoding RNAs that can repress the expression of protein-coding messenger RNAs (mRNAs) by binding to the 3{\textquoteright}-untranslated region (UTR) of the target. Genetic mutations such as single nucleotide variants (SNVs) in the 3{\textquoteright}-UTR of the mRNAs can disrupt miRNA regulation. In this study, we presented dbMTS, a database for miRNA target site (MTS) SNVs and their functional annotations. This database can help studies easily identify putative SNVs that affect miRNA targeting and facilitate the prioritization of their functional importance. dbMTS is freely available for academic use at http://database.liulab.science/dbMTS as a web service or a downloadable attached database of dbNSFP.

}, issn = {1098-1004}, doi = {10.1002/humu.24020}, author = {Li, Chang and Mou, Chengcheng and Swartz, Michael D and Yu, Bing and Bai, Yongsheng and Tu, Yicheng and Liu, Xiaoming} } @article {435, title = {FOXP3 mutations causing early-onset insulin-requiring diabetes but without other features of immune dysregulation, polyendocrinopathy, enteropathy, X-linked syndrome.}, journal = {Pediatr Diabetes}, volume = {19}, year = {2018}, month = {2018 05}, pages = {388-392}, abstract = {

Diabetes occurs in 1/90 000 to 1/160 000 births and when diagnosed under 6 months of age is very likely to have a primary genetic cause. FOXP3 encodes a transcription factor critical for T regulatory cell function and mutations are known to cause "immune dysregulation, polyendocrinopathy (including insulin-requiring diabetes), enteropathy, X-linked" (IPEX) syndrome. This condition is often fatal unless patients receive a bone-marrow transplant. Here we describe the phenotype of male neonates and infants who had insulin-requiring diabetes without other features of IPEX syndrome and were found to have mutations in FOXP3. Whole-exome or next generation sequencing of genes of interest was carried out in subjects with isolated neonatal diabetes without a known genetic cause. RT-PCR was carried out to investigate the effects on RNA splicing of a novel intronic splice-site variant. Four male subjects were found to have FOXP3 variants in the hemizygous state: p.Arg114Trp, p.Arg347His, p.Lys393Met, and c.1044+5G>A which was detected in 2 unrelated probands and in a brother diagnosed with diabetes at 2.1 years of age. Of these, p.Arg114Trp is likely a benign rare variant found in individuals of Ashkenazi Jewish ancestry and p.Arg347His has been previously described in patients with classic IPEX syndrome. The p.Lys393Met and c.1044+5G>A variants are novel to this study. RT-PCR studies of the c.1044+5G>A splice variant confirmed it affected RNA splicing by generating both a wild type and truncated transcript. We conclude that FOXP3 mutations can cause early-onset insulin-requiring diabetes with or without other features of IPEX syndrome.

}, keywords = {Diabetes Mellitus, Diabetes Mellitus, Type 1, Diarrhea, Forkhead Transcription Factors, Genetic Diseases, X-Linked, Humans, Immune System Diseases, Infant, Infant, Newborn, Male, Registries}, issn = {1399-5448}, doi = {10.1111/pedi.12612}, author = {Hwang, Jessica L and Park, Soo-Young and Ye, Honggang and Sanyoura, May and Pastore, Ashley N and Carmody, David and Del Gaudio, Daniela and Wilson, Janna F and Hanis, Craig L and Liu, Xiaoming and Atzmon, Gil and Glaser, Benjamin and Philipson, Louis H and Greeley, Siri Atma W} } @article {373, title = {Identification of Rare Variants in Metabolites of the Carnitine Pathway by Whole Genome Sequencing Analysis.}, journal = {Genet Epidemiol}, volume = {40}, year = {2016}, month = {2016 09}, pages = {486-91}, abstract = {

We use whole genome sequence data and rare variant analysis methods to investigate a subset of the human serum metabolome, including 16 carnitine-related metabolites that are important components of mammalian energy metabolism. Medium pass sequence data consisting of 12,820,347 rare variants and serum metabolomics data were available on 1,456 individuals. By applying a penalization method, we identified two genes FGF8 and MDGA2 with significant effects on lysine and cis-4-decenoylcarnitine, respectively, using Δ-AIC and likelihood ratio test statistics. Single variant analyses in these regions did not identify a single low-frequency variant (minor allele count > 3) responsible for the underlying signal. The results demonstrate the utility of whole genome sequence and innovative analyses for identifying candidate regions influencing complex phenotypes.

}, keywords = {Biomarkers, Carnitine, Female, Fibroblast Growth Factor 8, Genetic Variation, GPI-Linked Proteins, High-Throughput Nucleotide Sequencing, Humans, Linkage Disequilibrium, Lysine, Male, Metabolomics, Middle Aged, Neural Cell Adhesion Molecules, Polymorphism, Single Nucleotide, Sequence Analysis, DNA}, issn = {1098-2272}, doi = {10.1002/gepi.21980}, author = {Yazdani, Akram and Yazdani, Azam and Liu, Xiaoming and Boerwinkle, Eric} } @article {292, title = {Neonatal diabetes, gallbladder agenesis, duodenal atresia, and intestinal malrotation caused by a novel homozygous mutation in RFX6.}, journal = {Pediatr Diabetes}, volume = {15}, year = {2014}, month = {2014 Feb}, pages = {67-72}, abstract = {

Recently, bi-allelic mutations in the transcription factor RFX6 were described as the cause of a rare condition characterized by neonatal diabetes with pancreatic and biliary hypoplasia and duodenal/jejunal atresia. A male infant developed severe hyperglycemia (446 mg/dL) within 24 h of birth. Acute abdominal concerns by day five necessitated exploratory surgery that revealed duodenal atresia, gallbladder agenesis, annular pancreas and intestinal malrotation. He also exhibited chronic diarrhea and feeding intolerance, cholestatic jaundice, and subsequent liver failure. He died of sepsis at four months old while awaiting liver transplantation. The phenotype of neonatal diabetes with intestinal atresia and biliary agenesis clearly pointed to RFX6 as the causative gene; indeed, whole exome sequencing revealed a novel homozygous RFX6 mutation c.779A>C; p.Lys260Thr (K260T). This missense mutation also changes the consensus 5{\textquoteright} splice donor site before intron 7 and is thus predicted to cause disruption in splicing. Both parents, who were not known to be related, were heterozygous carriers. Targeted genetic testing based on consideration of phenotypic features may reveal a cause among the many genes now associated with heterogeneous forms of monogenic neonatal diabetes. Our study demonstrates the feasibility of using modern sequencing technology to identify one such rare cause. Continued research is needed to determine the possible cost-effectiveness of this approach, especially when clear phenotypic clues are absent. Further study of patients with RFX6 mutations should clarify its role in pancreatic, intestinal and enteroendocrine cellular development and explain features such as the diarrhea exhibited in our case.

}, keywords = {Abnormalities, Multiple, Congenital Abnormalities, Diabetes Mellitus, Type 1, Digestive System Abnormalities, DNA-Binding Proteins, Duodenal Obstruction, Fatal Outcome, Gallbladder, Humans, Infant, Infant, Newborn, Infant, Newborn, Diseases, Intestinal Atresia, Intestinal Volvulus, Male, Pancreas, Pancreatic Diseases, Regulatory Factor X Transcription Factors, Transcription Factors}, issn = {1399-5448}, doi = {10.1111/pedi.12063}, author = {Concepcion, Jennifer P and Reh, Christina S and Daniels, Mark and Liu, Xiaoming and Paz, Veronica P and Ye, Honggang and Highland, Heather M and Hanis, Craig L and Greeley, Siri Atma W} }