Whole-Exome Sequencing Identifies Novel Variants for Tooth Agenesis.

Tooth agenesis is a common craniofacial abnormality in humans and represents failure to develop 1 or more permanent teeth. Tooth agenesis is complex, and variations in about a dozen genes have been reported as contributing to the etiology. Here, we combined whole-exome sequencing, array-based genotyping, and linkage analysis to identify putative pathogenic variants in candidate disease genes for tooth agenesis in 10 multiplex Turkish families. Novel homozygous and heterozygous variants in LRP6, DKK1, LAMA3, and COL17A1 genes, as well as known variants in WNT10A, were identified as likely pathogenic in isolated tooth agenesis. Novel variants in KREMEN1 were identified as likely pathogenic in 2 families with suspected syndromic tooth agenesis. Variants in more than 1 gene were identified segregating with tooth agenesis in 2 families, suggesting oligogenic inheritance. Structural modeling of missense variants suggests deleterious effects to the encoded proteins. Functional analysis of an indel variant (c.3607+3_6del) in LRP6 suggested that the predicted resulting mRNA is subject to nonsense-mediated decay. Our results support a major role for WNT pathways genes in the etiology of tooth agenesis while revealing new candidate genes. Moreover, oligogenic cosegregation was suggestive for complex inheritance and potentially complex gene product interactions during development, contributing to improved understanding of the genetic etiology of familial tooth agenesis.

Phenotype expansion and development in Kosaki overgrowth syndrome.

We expand the Kosaki overgrowth syndrome (KOGS) phenotype by over 70% to include 24 unreported KOGS symptoms, in a first male patient, the third overall associated with the PDGFRB c.1751C>G p.(Pro584Arg) mutation. Eighteen of these symptoms are unique to our patient, the remaining six are shared with other patients. Of the 24 unreported features overall, 6 show marked phenotype evolution and varying time of onset. The triangular face detected at 14 months and long palpebral fissures with lateral ectropion at 4 years are present in other members of the cohort. The remaining 4 are unique to Patient 5: pronounced macrocephaly from birth, increasingly triangular anterior skull from 14 months, camptodactyly, emerging at 4 years and worsening joint contractures from 6 years. Compilation of all new symptoms reported here with published clinical data further identifies at least 18 clinical parameters common to all cases to date, encompassing both known KOGS-associated PDGFRB mutations. We therefore propose a set of 18 core KOGS symptoms, with 16 present in early childhood. These results should also impact diagnostic/prognostic scope, intervention and outcome potential for KOGS patients, particularly for developmentally progressive conditions such as scoliosis and myofibroma.

Genomic innovations, transcriptional plasticity and gene loss underlying the evolution and divergence of two highly polyphagous and invasive Helicoverpa pest species.

BACKGROUND: Helicoverpa armigera and Helicoverpa zea are major caterpillar pests of Old and New World agriculture, respectively. Both, particularly H. armigera, are extremely polyphagous, and H. armigera has developed resistance to many insecticides. Here we use comparative genomics, transcriptomics and resequencing to elucidate the genetic basis for their properties as pests. RESULTS: We find that, prior to their divergence about 1.5 Mya, the H. armigera/H. zea lineage had accumulated up to more than 100 more members of specific detoxification and digestion gene families and more than 100 extra gustatory receptor genes, compared to other lepidopterans with narrower host ranges. The two genomes remain very similar in gene content and order, but H. armigera is more polymorphic overall, and H. zea has lost several detoxification genes, as well as about 50 gustatory receptor genes. It also lacks certain genes and alleles conferring insecticide resistance found in H. armigera. Non-synonymous sites in the expanded gene families above are rapidly diverging, both between paralogues and between orthologues in the two species. Whole genome transcriptomic analyses of H. armigera larvae show widely divergent responses to different host plants, including responses among many of the duplicated detoxification and digestion genes. CONCLUSIONS: The extreme polyphagy of the two heliothines is associated with extensive amplification and neofunctionalisation of genes involved in host finding and use, coupled with versatile transcriptional responses on different hosts. H. armigera's invasion of the Americas in recent years means that hybridisation could generate populations that are both locally adapted and insecticide resistant.

Whole-exome sequencing points to considerable genetic heterogeneity of cerebral palsy.

Cerebral palsy (CP) is a common, clinically heterogeneous group of disorders affecting movement and posture. Its prevalence has changed little in 50 years and the causes remain largely unknown. The genetic contribution to CP causation has been predicted to be ~2%. We performed whole-exome sequencing of 183 cases with CP including both parents (98 cases) or one parent (67 cases) and 18 singleton cases (no parental DNA). We identified and validated 61 de novo protein-altering variants in 43 out of 98 (44%) case-parent trios. Initial prioritization of variants for causality was by mutation type, whether they were known or predicted to be deleterious and whether they occurred in known disease genes whose clinical spectrum overlaps CP. Further, prioritization used two multidimensional frameworks-the Residual Variation Intolerance Score and the Combined Annotation-dependent Depletion score. Ten de novo mutations in three previously identified disease genes (TUBA1A (n=2), SCN8A (n=1) and KDM5C (n=1)) and in six novel candidate CP genes (AGAP1, JHDM1D, MAST1, NAA35, RFX2 and WIPI2) were predicted to be potentially pathogenic for CP. In addition, we identified four predicted pathogenic, hemizygous variants on chromosome X in two known disease genes, L1CAM and PAK3, and in two novel candidate CP genes, CD99L2 and TENM1. In total, 14% of CP cases, by strict criteria, had a potentially disease-causing gene variant. Half were in novel genes. The genetic heterogeneity highlights the complexity of the genetic contribution to CP. Function and pathway studies are required to establish the causative role of these putative pathogenic CP genes.

Riboflavin metabolism in the hypothyroid human adult.

It had been shown that thyroxine regulates the conversion of riboflavin to riboflavin mononucleotide and flavin adenine dinucleotide (FAD) in laboratory animals. In the hypothyroid rat, the flavin adenine dinucleotide level of the liver decreases to levels observed in riboflavin deficiency. We have shown that in six hypothyroid human adults, the activity of erythrocyte glutathione reductase, an accessible FAD-containing enzyme, is decreased to levels observed during riboflavin deficiency. Thyroxine therapy resulted in normal levels of this enzyme while the subjects were on a controlled dietary regimen. This demonstrates that thyroid hormone regulates the enzymatic conversion of riboflavin to its active coenzyme forms in the human adult.

Pancreatitis in a native American Indian population.

We have studied pancreatitis in a population of Southwestern American Indians where gallstones are frequent, alcohol consumption is presumably high, but where smoking is an uncommon habit. Over a 5-year period, 131 cases of pancreatitis (65 males, 66 females) were observed: 66 (50%) were thought to be biliary pancreatitis, 54 cases (41%) alcoholic pancreatitis, and 5 cases (4%) were caused by injuries. In 6 cases (5%) no definite cause was found. Smoking appeared to be increased in male subjects with alcoholic pancreatitis when compared to subjects with alcoholic liver cirrhosis--a group with similar drinking habits. (Adjusted odds ratio = 12.5, p = 0.008). No such relationship was observed for females. Our findings suggest that in this population smoking may be an additional important risk factor for male subjects with alcoholic pancreatitis.

Energy expenditure in chronic alcoholics with and without liver disease.

Chronic alcoholism activates metabolic pathways, resulting in wasteful expenditure of energy (Pirola and Lieber, J Nutr 1975;105:1544-8). To study this hypothesis, we measured oxygen consumption (VO2), carbon dioxide production (VCO2), and resting energy expenditure (MREE) utilizing indirect calorimetry in 8 chronic alcoholics with (group I) and 11 chronic alcoholics without (group II) clinical or biochemical evidence of alcoholic liver disease. Seven healthy volunteers served as controls. A statistically increased MREE was observed in group II subjects (p less than 0.05, MREE 999.7 +/- 111.4 kcal X day X m2) as compared to normals (MREE 842.3 +/- 42.1 kcal X day X m2) and group I subjects (MREE 813.4 +/- 101.4 kcal X day X m2). VO2 and VCO2 were also significantly higher (p less than 0.05) in group II than in group I and normals. The predicted resting energy expenditure as calculated by the Harris-Benedict equation was similar in both groups and normals. Theories to explain the increased MREE in group II subjects are presented.

Clinical zinc deficiency during long-term total enteral nutrition.

Zinc deficiency during long-term total parenteral nutrition has been well reported in the literature. However, there is limited information available on zinc deficiency occurring during total enteral nutrition. Two cases of clinical zinc deficiency in patients on long-term enteral feedings are presented. Nutritional assessment of these two patients on admission revealed hypoalbuminemic malnutrition. Nutritional support in the form of nasogastric tube feedings were initiated in both patients due to altered mental status. The formula used was Ensure (Ross Labs, Columbus, OH), which provided greater than 150% of the RDA for zinc. However, four months and seven months after initiation of adequate nutritional support, both patients developed skin rashes around the groin and under the breasts and axilla. Serum zinc levels were depressed in both patients, to 42 and 54 mg/dL, respectively (normal for the authors' laboratory, 66 to 120 mg/dL). Supplementation with zinc sulfate 220 mg per day via nasogastric tube resulted in disappearance of the rash with return of serum zinc to normal levels. The authors suggest close observation of patients on long-term enteral nutrition for clinical manifestation of zinc deficiency, especially an unexplained skin rash. Further studies are needed to establish minimum daily zinc requirements in patients on long-term enteral feedings.