Scientific Publications

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Hypospadias Prevalence and Trends in International Birth Defect Surveillance Systems, 1980-2010

Yu X, Nassar N, Mastroiacovo P, Canfield M, Groisman B, Bermejo-Sánchez E, Ritvanen A, Kiuru-Kuhlefelt S, Benavides A, Sipek A, Pierini A, Bianchi F, Källén K, Gatt M, Morgan M, Tucker D, Canessa MA, Gajardo R, Mutchinick OM, Szabova E, Csáky-Szunyogh M, Tagliabue G, Cragan JD, Nembhard WN, Rissmann A, Goetz D, Bower C, Baynam G, Lowry RB, Leon JA, Luo W, Rouleau J, Zarante I, Fernandez N, Amar E, Dastgiri S, Contiero P, Martínez-de-Villarreal LE, Borman B, Bergman JEH, de Walle HEK, Hobbs CA, Nance AE, Agopian AJ. H

Eur Urol. 2019 Oct;76(4):482-490. doi: 10.1016/j.eururo.2019.06.027. Epub 2019 Jul 9. ABSTRACT BACKGROUND: Hypospadias is a common male birth defect that has shown widespread variation in reported prevalence estimates. Many countries have reported increasing trends over recent decades. OBJECTIVE: To analyze the prevalence and trends of hypospadias for 27 international programs over a 31-yr period. DESIGN, SETTING, AND PARTICIPANTS: The study population included live births, stillbirths, and elective terminations of pregnancy diagnosed with hypospadias during 1980-2010 from 27 surveillance programs around the world. OUTCOME MEASUREMENTS AND STATISTICAL ANALYSIS: We used joinpoint regression to analyze changes over time in international total prevalence of hypospadias across programs, prevalence for each specific program, and prevalence across different degrees of severity of hypospadias. RESULTS AND LIMITATIONS: The international total prevalence of hypospadias for all years was 20.9 (95% confidence interval: 19.2-22.6) per 10000 births. The prevalence for each program ranged from 2.1 to 39.1 per 10000 births. The international total prevalence increased 1.6 times during the study period, by 0.25 cases per 10000 births per year (p<0.05). When analyzed separately, there were increasing trends for first-, second-, and third-degree hypospadias during the early 1990s to mid-2000s. The majority of programs (61.9%) had a significantly increasing trend during many of the years evaluated. Limitations include known differences in data collection methods across programs. CONCLUSIONS: Although there have been changes in clinical practice and registry ascertainment over time in some countries, the consistency in the observed increasing trends across many programs and by degrees of severity suggests that the total prevalence of hypospadias may be increasing in many countries. This observation is contrary to some previous reports that suggested that the total prevalence of hypospadias was no longer increasing in recent decades. PATIENT SUMMARY: We report on the prevalence and trends of hypospadias among 27 birth defect surveillance systems, which indicate that the prevalence of hypospadias continues to increase internationally. PMID:31300237 | PMC:PMC7265200 | DOI:10.1016/j.eururo.2019.06.027

July 14, 2019

NSUN2 introduces 5-methylcytosines in mammalian mitochondrial tRNAs

Van Haute L, Lee SY, McCann BJ, Powell CA, Bansal D, Vasiliauskaitė L, Garone C, Shin S, Kim JS, Frye M, Gleeson JG, Miska EA, Rhee HW, Minczuk M.

Nucleic Acids Res. 2019 Sep 19;47(16):8720-8733. doi: 10.1093/nar/gkz559. ABSTRACT Expression of human mitochondrial DNA is indispensable for proper function of the oxidative phosphorylation machinery. The mitochondrial genome encodes 22 tRNAs, 2 rRNAs and 11 mRNAs and their post-transcriptional modification constitutes one of the key regulatory steps during mitochondrial gene expression. Cytosine-5 methylation (m5C) has been detected in mitochondrial transcriptome, however its biogenesis has not been investigated in details. Mammalian NOP2/Sun RNA Methyltransferase Family Member 2 (NSUN2) has been characterized as an RNA methyltransferase introducing m5C in nuclear-encoded tRNAs, mRNAs and microRNAs and associated with cell proliferation and differentiation, with pathogenic variants in NSUN2 being linked to neurodevelopmental disorders. Here we employ spatially restricted proximity labelling and immunodetection to demonstrate that NSUN2 is imported into the matrix of mammalian mitochondria. Using three genetic models for NSUN2 inactivation-knockout mice, patient-derived fibroblasts and CRISPR/Cas9 knockout in human cells-we show that NSUN2 is necessary for the generation of m5C at positions 48, 49 and 50 of several mammalian mitochondrial tRNAs. Finally, we show that inactivation of NSUN2 does not have a profound effect on mitochondrial tRNA stability and oxidative phosphorylation in differentiated cells. We discuss the importance of the newly discovered function of NSUN2 in the context of human disease. PMID:31276587 | PMC:PMC6822013 | DOI:10.1093/nar/gkz559

July 6, 2019

DYRK1A-related intellectual disability: a syndrome associated with congenital anomalies of the kidney and urinary tract

Blackburn ATM, Bekheirnia N, Uma VC, Corkins ME, Xu Y, Rosenfeld JA, Bainbridge MN, Yang Y, Liu P, Madan-Khetarpal S, Delgado MR, Hudgins L, Krantz I, Rodriguez-Buritica D, Wheeler PG, Al-Gazali L, Mohamed Saeed Mohamed Al Shamsi A, Gomez-Ospina N, Chao HT, Mirzaa GM, Scheuerle AE, Kukolich MK, Scaglia F, Eng C, Willsey HR, Braun MC, Lamb DJ, Miller RK, Bekheirnia MR.

Genet Med. 2019 Dec;21(12):2755-2764. doi: 10.1038/s41436-019-0576-0. Epub 2019 Jul 2. ABSTRACT PURPOSE: Haploinsufficiency of DYRK1A causes a recognizable clinical syndrome. The goal of this paper is to investigate congenital anomalies of the kidney and urinary tract (CAKUT) and genital defects (GD) in patients with DYRK1A variants. METHODS: A large database of clinical exome sequencing (ES) was queried for de novo DYRK1A variants and CAKUT/GD phenotypes were characterized. Xenopus laevis (frog) was chosen as a model organism to assess Dyrk1a’s role in renal development. RESULTS: Phenotypic details and variants of 19 patients were compiled after an initial observation that one patient with a de novo pathogenic variant in DYRK1A had GD. CAKUT/GD data were available from 15 patients, 11 of whom presented with CAKUT/GD. Studies in Xenopus embryos demonstrated that knockdown of Dyrk1a, which is expressed in forming nephrons, disrupts the development of segments of embryonic nephrons, which ultimately give rise to the entire genitourinary (GU) tract. These defects could be rescued by coinjecting wild-type human DYRK1A RNA, but not with DYRK1AR205* or DYRK1AL245R RNA. CONCLUSION: Evidence supports routine GU screening of all individuals with de novo DYRK1A pathogenic variants to ensure optimized clinical management. Collectively, the reported clinical data and loss-of-function studies in Xenopus substantiate a novel role for DYRK1A in GU development. PMID:31263215 | PMC:PMC6895419 | DOI:10.1038/s41436-019-0576-0

July 3, 2019

Rapid Whole Genome Sequencing Has Clinical Utility in Children in the PICU

Sanford EF, Clark MM, Farnaes L, Williams MR, Perry JC, Ingulli EG, Sweeney NM, Doshi A, Gold JJ, Briggs B, Bainbridge MN, Feddock M, Watkins K, Chowdhury S, Nahas SA, Dimmock DP, Kingsmore SF, Coufal NG; RCIGM Investigators.

Pediatr Crit Care Med. 2019 Nov;20(11):1007-1020. doi: 10.1097/PCC.0000000000002056. ABSTRACT OBJECTIVES: Genetic disorders are a leading contributor to mortality in the neonatal ICU and PICU in the United States. Although individually rare, there are over 6,200 single-gene diseases, which may preclude a genetic diagnosis prior to ICU admission. Rapid whole genome sequencing is an emerging method of diagnosing genetic conditions in time to affect ICU management of neonates; however, its clinical utility has yet to be adequately demonstrated in critically ill children. This study evaluates next-generation sequencing in pediatric critical care. DESIGN: Retrospective cohort study. SETTING: Single-center PICU in a tertiary children’s hospital. PATIENTS: Children 4 months to 18 years admitted to the PICU who were nominated between July 2016 and May 2018. INTERVENTIONS: Rapid whole genome sequencing with targeted phenotype-driven analysis was performed on patients and their parents, when parental samples were available. MEASUREMENTS AND MAIN RESULTS: A molecular diagnosis was made by rapid whole genome sequencing in 17 of 38 children (45%). In four of the 17 patients (24%), the genetic diagnoses led to a change in management while in the PICU, including genome-informed changes in pharmacotherapy and transition to palliative care. Nine of the 17 diagnosed children (53%) had no dysmorphic features or developmental delay. Eighty-two percent of diagnoses affected the clinical management of the patient and/or family after PICU discharge, including avoidance of biopsy, administration of factor replacement, and surveillance for disorder-related sequelae. CONCLUSIONS: This study demonstrates a retrospective evaluation for undiagnosed genetic disease in the PICU and clinical utility of rapid whole genome sequencing in a portion of critically ill children. Further studies are needed to identify PICU patients who will benefit from rapid whole genome sequencing early in PICU admission when the underlying etiology is unclear. PMID:31246743 | PMC:PMC6832787 | DOI:10.1097/PCC.0000000000002056

June 28, 2019
Infant MortalityrWGSrWGS Efficacy

Neonatal diabetes mellitus due to a novel variant in the INS gene

Laurenzano SE, McFall C, Nguyen L, Savla D, Coufal NG, Wright MS, Tokita M, Dimmock D, Kingsmore SF, Newfield RS.

Cold Spring Harb Mol Case Stud. 2019 Aug 1;5(4):a004085. doi: 10.1101/mcs.a004085. Print 2019 Aug. ABSTRACT Neonatal diabetes mellitus (NDM) is a rare condition that presents with diabetes in the first few months of life. The treatment of NDM may differ depending on the genetic etiology, with numerous studies showing the benefit of sulfonylurea therapy in cases caused by mutations in KCNJ11 or ABCC8 Mutations in the insulin gene (INS) have also been identified as causes of NDM; these cases are generally best treated with insulin alone. We report a case of a female infant born small for gestational age (SGA) at late preterm diagnosed with NDM at 7 wk of life who was found by rapid whole-genome sequencing to harbor a novel de novo c.26C>G (p.Pro9Arg) variant in the INS gene. She presented with diabetic ketoacidosis, which responded to insulin therapy. She did not respond to empiric trial of sulfonylurea therapy early in her hospital course, and it was discontinued once a genetic diagnosis was made. Early genetic evaluation in patients presenting with NDM is essential to optimize therapeutic decision-making. PMID:31196892 | PMC:PMC6672029 | DOI:10.1101/mcs.a004085

June 15, 2019

Further phenotypic characterization of Kaufman oculocerebrofacial syndrome: report of five new cases and literature review

Galarreta CI, Wigby KM, Jones MC.

Clin Dysmorphol. 2019 Oct;28(4):175-183. doi: 10.1097/MCD.0000000000000282. ABSTRACT Kaufman oculocerebrofacial syndrome is a rare autosomal recessive disorder caused by biallelic variants in UBE3B. Kaufman oculocerebrofacial syndrome is characterized by a recognizable pattern of malformations including moderate to severe intellectual disability, growth deficiency, microcephaly and a distinctive facial gestalt. Common craniofacial features include short upslanting palpebral fissures, blepharophimosis or ptosis, ear anomalies, hearing loss, palate anomalies and stridor/laryngomalacia. The aim of this study was to describe the phenotypic features and the genotype of five new individuals from three unrelated families, and to review systematically the published information of 26 cases. The main features are summarized contributing to further characterize the natural history of the disease. Novel phenotypic features and two novel pathogenic variants in UBE3B are reported: A splice site variant (c.2569-1G > C) and a nonsense variant (c.518C > A, p.Ser173Ter). Kaufman oculocerebrofacial syndrome is likely an underdiagnosed disorder which can be clinically recognized based on its distinctive facial gestalt and relatively homogenous natural history. PMID:31162149 | DOI:10.1097/MCD.0000000000000282

June 5, 2019

Diagnosis of genetic diseases in seriously ill children by rapid whole-genome sequencing and automated phenotyping and interpretation

Michelle M Clark, Amber Hildreth, Sergey Batalov, Yan Ding, Shimul Chowdhury, Kelly Watkins, Katarzyna Ellsworth, Brandon Camp, Cyrielle I Kint, Calum Yacoubian 5, Lauge Farnaes, Matthew N Bainbridge, Curtis Beebe, Joshua J A Braun, Margaret Bray, Jeanne Carroll, Julie A Cakici, Sara A Caylor, Christina Clarke, Mitchell P Creed, Jennifer Friedman, Alison Frith, Richard Gain, Mary Gaughran, Shauna George, Sheldon Gilmer, Joseph Gleeson, Jeremy Gore, Haiying Grunenwald, Raymond L Hovey, Marie L Janes, Kejia Lin, Paul D McDonagh, Kyle McBride, Patrick Mulrooney, Shareef Nahas, Daeheon Oh, Albert Oriol, Laura Puckett, Zia Rady, Martin G Reese, Julie Ryu, Lisa Salz, Erica Sanford, Lawrence Stewart, Nathaly Sweeney, Mari Tokita, Luca Van Der Kraan, Sarah White, Kristen Wigby, Brett Williams, Terence Wong, Meredith S Wright, Catherine Yamada, Peter Schols, John Reynders, Kevin Hall, David Dimmock, Narayanan Veeraraghavan, Thomas Defay 8, Stephen F Kingsmore

Sci Transl Med. 2019 Apr 24;11(489):eaat6177. doi: 10.1126/scitranslmed.aat6177. ABSTRACT By informing timely targeted treatments, rapid whole-genome sequencing can improve the outcomes of seriously ill children with genetic diseases, particularly infants in neonatal and pediatric intensive care units (ICUs). The need for highly qualified professionals to decipher results, however, precludes widespread implementation. We describe a platform for population-scale, provisional diagnosis of genetic diseases with automated phenotyping and interpretation. Genome sequencing was expedited by bead-based genome library preparation directly from blood samples and sequencing of paired 100-nt reads in 15.5 hours. Clinical natural language processing (CNLP) automatically extracted children’s deep phenomes from electronic health records with 80% precision and 93% recall. In 101 children with 105 genetic diseases, a mean of 4.3 CNLP-extracted phenotypic features matched the expected phenotypic features of those diseases, compared with a match of 0.9 phenotypic features used in manual interpretation. We automated provisional diagnosis by combining the ranking of the similarity of a patient’s CNLP phenome with respect to the expected phenotypic features of all genetic diseases, together with the ranking of the pathogenicity of all of the patient’s genomic variants. Automated, retrospective diagnoses concurred well with expert manual interpretation (97% recall and 99% precision in 95 children with 97 genetic diseases). Prospectively, our platform correctly diagnosed three of seven seriously ill ICU infants (100% precision and recall) with a mean time saving of 22:19 hours. In each case, the diagnosis affected treatment. Genome sequencing with automated phenotyping and interpretation in a median of 20:10 hours may increase adoption in ICUs and, thereby, timely implementation of precise treatments. PMID:31019026 | DOI:10.1126/scitranslmed.aat6177

April 26, 2019
Infant MortalityRare Disease

Effect of Sociodemographic Factors on Uptake of a Patient-Facing Information Technology Family Health History Risk Assessment Platform

Wu RR, Myers RA, Buchanan AH, Dimmock D, Fulda KG, Haller IV, Haga SB, Harry ML, McCarty C, Neuner J, Rakhra-Burris T, Sperber N, Voils CI, Ginsburg GS, Orlando LA.

Appl Clin Inform. 2019 Mar;10(2):180-188. doi: 10.1055/s-0039-1679926. Epub 2019 Mar 13. ABSTRACT OBJECTIVE: Investigate sociodemographic differences in the use of a patient-facing family health history (FHH)-based risk assessment platform. METHODS: In this large multisite trial with a diverse patient population, we evaluated the relationship between sociodemographic factors and FHH health risk assessment uptake using an information technology (IT) platform. The entire study was administered online, including consent, baseline survey, and risk assessment completion. We used multivariate logistic regression to model effect of sociodemographic factors on study progression. Quality of FHH data entered as defined as relatives: (1) with age of onset reported on relevant conditions; (2) if deceased, with cause of death and (3) age of death reported; and (4) percentage of relatives with medical history marked as unknown was analyzed using grouped logistic fixed effect regression. RESULTS: A total of 2,514 participants consented with a mean age of 57 and 10.4% minority. Multivariate modeling showed that progression through study stages was more likely for younger (p-value = 0.005), more educated (p-value = 0.004), non-Asian (p-value = 0.009), and female (p-value = 0.005) participants. Those with lower health literacy or information-seeking confidence were also less likely to complete the study. Most significant drop-out occurred during the risk assessment completion phase. Overall, quality of FHH data entered was high with condition’s age of onset reported 87.85%, relative’s cause of death 85.55% and age of death 93.76%, and relative’s medical history marked as unknown 19.75% of the time. CONCLUSION: A demographically diverse population was able to complete an IT-based risk assessment but there were differences in attrition by sociodemographic factors. More attention should be given to ensure end-user functionality of health IT and leverage electronic medical records to lessen patient burden. PMID:30866001 | PMC:PMC6415985 | DOI:10.1055/s-0039-1679926

March 14, 2019

Biallelic mutations in valyl-tRNA synthetase gene VARS are associated with a progressive neurodevelopmental epileptic encephalopathy

Friedman J, Smith DE, Issa MY, Stanley V, Wang R, Mendes MI, Wright MS, Wigby K, Hildreth A, Crawford JR, Koehler AE, Chowdhury S, Nahas S, Zhai L, Xu Z, Lo WS, James KN, Musaev D, Accogli A, Guerrero K, Tran LT, Omar TEI, Ben-Omran T, Dimmock D, Kingsmore SF, Salomons GS, Zaki MS, Bernard G, Gleeson JG. 

Nat Commun. 2019 Feb 12;10(1):707. doi: 10.1038/s41467-018-07067-3. ABSTRACT Aminoacyl-tRNA synthetases (ARSs) function to transfer amino acids to cognate tRNA molecules, which are required for protein translation. To date, biallelic mutations in 31 ARS genes are known to cause recessive, early-onset severe multi-organ diseases. VARS encodes the only known valine cytoplasmic-localized aminoacyl-tRNA synthetase. Here, we report seven patients from five unrelated families with five different biallelic missense variants in VARS. Subjects present with a range of global developmental delay, epileptic encephalopathy and primary or progressive microcephaly. Longitudinal assessment demonstrates progressive cortical atrophy and white matter volume loss. Variants map to the VARS tRNA binding domain and adjacent to the anticodon domain, and disrupt highly conserved residues. Patient primary cells show intact VARS protein but reduced enzymatic activity, suggesting partial loss of function. The implication of VARS in pediatric neurodegeneration broadens the spectrum of human diseases due to mutations in tRNA synthetase genes. PMID:30755602 | PMC:PMC6372641 | DOI:10.1038/s41467-018-07067-3

February 14, 2019


Blacklisting variants common in private cohorts but not in public databases optimizes human exome analysis

Maffucci P, Bigio B, Rapaport F, Cobat A, Borghesi A, Lopez M, Patin E, Bolze A, Shang L, Bendavid M, Scott EM, Stenson PD, Cunningham-Rundles C, Cooper DN, Gleeson JG, Fellay J, Quintana-Murci L, Casanova JL, Abel L, Boisson B, Itan Y.

Proc Natl Acad Sci U S A. 2019 Jan 15;116(3):950-959. doi: 10.1073/pnas.1808403116. Epub 2018 Dec 27. ABSTRACT Computational analyses of human patient exomes aim to filter out as many nonpathogenic genetic variants (NPVs) as possible, without removing the true disease-causing mutations. This involves comparing the patient’s exome with public databases to remove reported variants inconsistent with disease prevalence, mode of inheritance, or clinical penetrance. However, variants frequent in a given exome cohort, but absent or rare in public databases, have also been reported and treated as NPVs, without rigorous exploration. We report the generation of a blacklist of variants frequent within an in-house cohort of 3,104 exomes. This blacklist did not remove known pathogenic mutations from the exomes of 129 patients and decreased the number of NPVs remaining in the 3,104 individual exomes by a median of 62%. We validated this approach by testing three other independent cohorts of 400, 902, and 3,869 exomes. The blacklist generated from any given cohort removed a substantial proportion of NPVs (11-65%). We analyzed the blacklisted variants computationally and experimentally. Most of the blacklisted variants corresponded to false signals generated by incomplete reference genome assembly, location in low-complexity regions, bioinformatic misprocessing, or limitations inherent to cohort-specific private alleles (e.g., due to sequencing kits, and genetic ancestries). Finally, we provide our precalculated blacklists, together with ReFiNE, a program for generating customized blacklists from any medium-sized or large in-house cohort of exome (or other next-generation sequencing) data via a user-friendly public web server. This work demonstrates the power of extracting variant blacklists from private databases as a specific in-house but broadly applicable tool for optimizing exome analysis. PMID:30591557 | PMC:PMC6338851 | DOI:10.1073/pnas.1808403116

December 29, 2018

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