Exome sequencing reveals novel genetic loci influencing obesity-related traits in Hispanic children: Novel Obesity Loci in Hispanic Children

Perform whole exome sequencing in 928 Hispanic children and identify variants and genes associated with childhood obesity

Deleterious Heteroplasmic Mitochondrial Mutations are associated With an increased Risk of Overall and Cancer-Specific Mortality

Mitochondria carry their own circular genome and disruption of the mitochondrial genome is associated with various aging-related diseases. Unlike the nuclear genome, mitochondrial DNA (mtDNA) can be present at 1000 s to 10,000 s copies in somatic cells and variants may exist in a state of heteroplasmy, where only a fraction of the DNA molecules harbors a particular variant. We quantify mtDNA heteroplasmy in 194,871 participants in the UK Biobank and find that heteroplasmy is associated with a 1.5-fold increased risk of all-cause mortality. Additionally, we functionally characterize mtDNA single nucleotide variants (SNVs) using a constraint-based score, mitochondrial local constraint score sum (MSS) and find it associated with all-cause mortality, and with the prevalence and incidence of cancer and cancer-related mortality, particularly leukemia. These results indicate that mitochondria may have a functional role in certain cancers, and mitochondrial heteroplasmic SNVs may serve as a prognostic marker for cancer, especially for leukemia

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

A T(5;16) Translocation Is The Likely Driver Of A Syndrome With Ambiguous Genitalia, Facial Dysmorphism, Intellectual Disability, And Speech Delay

Genetic studies grounded on monogenic paradigms have accelerated both gene discovery and molecular diagnosis. At the same time, complex genomic rearrangements are also appreciated as potent drivers of disease pathology. Here, we report two male siblings with a dysmorphic face, ambiguous genitalia, intellectual disability, and speech delay. Through quad-based whole-exome sequencing and concomitant molecular cytogenetic testing, we identified two copy-number variants (CNVs) in both affected individuals likely arising from a balanced translocation: a 13.5-Mb duplication on Chromosome 16 (16q23.1 → 16qter) and a 7.7-Mb deletion on Chromosome 5 (5p15.31 → 5pter), as well as a hemizygous missense variant in CXorf36 (also known as DIA1R). The 5p terminal deletion has been associated previously with speech delay, whereas craniofacial dysmorphia and genital/urinary anomalies have been reported in patients with a terminal duplication of 16q. However, dosage changes in either genomic region alone could not account for the overall clinical presentation in our family; functional testing of CXorf36 in zebrafish did not induce defects in neurogenesis or the craniofacial skeleton. Notably, literature and database analysis revealed a similar dosage disruption in two siblings with extensive phenotypic overlap with our patients. Taken together, our data suggest that dosage perturbation of genes within the two chromosomal regions likely drives the syndromic manifestations of our patients and highlight how multiple genetic lesions can contribute to complex clinical pathologies.PubMe

Whole Exome Sequencing Identifies Novel Genes for Fetal Hemoglobin Response to Hydroxyurea in Children with Sickle Cell Anemia

<div><p>Hydroxyurea has proven efficacy in children and adults with sickle cell anemia (SCA), but with considerable inter-individual variability in the amount of fetal hemoglobin (HbF) produced. Sibling and twin studies indicate that some of that drug response variation is heritable. To test the hypothesis that genetic modifiers influence pharmacological induction of HbF, we investigated phenotype-genotype associations using whole exome sequencing of children with SCA treated prospectively with hydroxyurea to maximum tolerated dose (MTD). We analyzed 171 unrelated patients enrolled in two prospective clinical trials, all treated with dose escalation to MTD. We examined two MTD drug response phenotypes: HbF (final %HbF minus baseline %HbF), and final %HbF. Analyzing individual genetic variants, we identified multiple low frequency and common variants associated with HbF induction by hydroxyurea. A validation cohort of 130 pediatric sickle cell patients treated to MTD with hydroxyurea was genotyped for 13 non-synonymous variants with the strongest association with HbF response to hydroxyurea in the discovery cohort. A coding variant in <i>Spalt-like transcription factor</i>, or <i>SALL2</i>, was associated with higher final HbF in this second independent replication sample and <i>SALL2</i> represents an outstanding novel candidate gene for further investigation. These findings may help focus future functional studies and provide new insights into the pharmacological HbF upregulation by hydroxyurea in patients with SCA.</p></div

Variants associated with ΔHbF on hydroxyurea.

<p>Variants selected were predicted damaging, with a p-value <0.001 in the discovery cohort, n = 171, composed of patients from HUSTLE and SWiTCH trials.</p><p>Variants associated with ΔHbF on hydroxyurea.</p

Effect of <i>SALL2</i> variant rs61743453 on HbF response to hydroxyurea.

<p>A, Effect of rs61743453 on delta HbF in discovery cohort. B, Effect of rs61743453 on MTD HbF in validation cohort. Variant refers to the Pro840Arg variant; no individuals were homozygous for this change.</p

Variants associated with final HbF on hydroxyurea.

<p>Variants selected were predicted damaging, with a p-value <0.001 in the discovery cohort, n = 171, composed of patients from HUSTLE and SWiTCH trials.</p><p>Variants associated with final HbF on hydroxyurea.</p

Comparison of discovery and validation cohorts.

<p>A, Baseline, or endogenous HbF for the discovery cohort is shown in binned histogram, and distribution of baseline HbF in validation cohort by a line plot. B, Delta HbF for the discovery cohort is shown in binned histogram, and distribution of delta HbF in validation cohort by a line plot. C, Final, or MID HbF for the discovery cohort is shown in binned histogram, and distribution of final, or MID in validation cohort by a line plot.</p

Comparison of discovery and validation cohorts.

<p>WBC: white blood cell count; ANC: absolute neutrophil count; ARC: absolute reticulocyte count; MCV: mean corpuscular volume; HU: hydroxyurea.</p><p>The discovery cohort was composed of 120 patients from HUSTLE and 51 from SWiTCH. The validation cohort was collected from patients treated at TCCH.</p><p>Comparison of discovery and validation cohorts.</p