Post-mortem diagnosis of Pompe disease by exome sequencing in a Moroccan family: a case report.

J Med Case Rep. 2018 Oct 29;12(1):322

Authors: Adadi N, Sahli M, Egéa G, Ratbi I, Taoudi M, Zniber L, Jdioui W, El Mouatassim S, Sefiani A

Abstract
BACKGROUND: Pompe disease is an autosomal recessive lysosomal storage disorder characterized by progressive myopathy with proximal muscle weakness, respiratory muscle dysfunction, and cardiomyopathy. Its prevalence ranges between 1/9000 and 1/40,000. It is caused by compound heterozygous or homozygous mutations in the GAA gene, which encodes for the lysosomal enzyme alpha-glucosidase, required for the degrading of lysosomal glycogen.
CASE PRESENTATION: In this study, we report the case of a Moroccan consanguineous family with hypertrophic cardiomyopathy and sudden cardiac deaths at an early age; our patient was a 7-month-old Moroccan girl. Whole exome sequencing identified the deleterious homozygous mutation c.236_246delCCACACAGTGC (p.Pro79ArgfsX13) of GAA gene leading to a post-mortem diagnosis of Pompe disease.
CONCLUSION: The identification of the genetic substrate in our patient, the daughter, confirmed the clinical diagnosis of Pompe disease and allowed us to provide appropriate genetic counseling to the family for future pregnancies.

PMID: 30371346 [PubMed - in process]

Population data improves variant interpretation in autosomal dominant polycystic kidney disease.

Genet Med. 2018 Oct 29;:

Authors: Mallawaarachchi AC, Furlong TJ, Shine J, Harris PC, Cowley MJ

Abstract
PURPOSE: Autosomal dominant polycystic kidney disease (ADPKD) is a common adult-onset monogenic disorder, with prevalence of 1/1000. Population databases including ExAC have improved pathogenic variant prioritization in many diseases. Due to pseudogene homology of PKD1, the predominant ADPKD disease gene, and the variable disease severity and age of onset, we aimed to investigate the utility of ExAC for variant assessment in ADPKD.
METHODS: We assessed coverage and variant quality in the ExAC cohort and combined allele frequency and age data from the ExAC database (n = 60,706) with curated variants from 2000 ADPKD pedigrees (ADPKD Mutation Database).
RESULTS: Seventy-six percent of PKD1 and PKD2 were sequenced adequately for variant discovery and variant quality was high in ExAC. In ExAC, we identified 25 truncating and 393 previously reported disease-causing variants in PKD1 and PKD2, 6.9-fold higher than expected. Fifty-four different variants, previously classified as disease-causing, were observed in ≥5 participants in ExAC.
CONCLUSION: Our study demonstrates that many previously implicated disease-causing variants are too common, challenging their pathogenicity, or penetrance. The presence of protein-truncating variants in older participants in ExAC demonstrates the complexity of variant classification and highlights need for further study of prevalence and penetrance of this common monogenic disease.

PMID: 30369598 [PubMed - as supplied by publisher]

Association study of frameshift and splice variant polymorphisms with risk of idiopathic recurrent pregnancy loss.

Mol Med Rep. 2018 Aug;18(2):2417-2426

Authors: Lee HA, Ahn EH, Kim JH, Kim JO, Ryu CS, Lee JY, Cho SH, Lee WS, Kim NK

Abstract
Recurrent pregnancy loss (RPL) is defined as ≥2 consecutive pregnancy losses, and can be caused by various factors, including genetics, chromosomal abnormalities, thrombophilia, immune disorders, nutritional factors, environmental factors, psychological stress or maternal infections; however, as many as 50% of RPL cases are idiopathic. In the present study, the role of genetic polymorphisms in RPL was investigated. Four gene polymorphisms were selected by whole exome sequencing, including membrane spanning 4‑domains A14 (MS4A14)D>I (rs3217518), solute carrier family 2 member 7 (SLC2A7)D>I (rs60746313), pregnancy specific β‑1‑glycoprotein 9 (PSG9)C>T (rs3746297) and ATP binding cassette subfamily B member 5 (ABCB5)C>G (rs17143187), and the aim was to investigate their association with RPL in Korean women. Genotyping was performed using polymerase chain reaction‑restriction fragment length polymorphism assay. Allele combination analysis revealed that the four‑allele combination I‑D‑T‑G, (MS4A14/SLC2A7/PSG9/ABCB5) was associated with a decreased risk for RPL. Interaction analysis demonstrated that the following genotypes: MS4A14 DI+II, SLC2A DI+II and ABCB 5 CG+GG, were associated with a prothrombin time ≥12 sec and with RPL risk. It may be concluded that the four gene polymorphisms do not affect RPL individually, but are associated with RPL when in combination with other genes or blood coagulation factors. Notably, the MS4A14 I allele, with a prothrombin time ≥12 sec, may be a potential biomarker for diagnosis, prevention and prognosis of RPL.

PMID: 29956771 [PubMed - indexed for MEDLINE]

Exome and genome sequencing in reproductive medicine.

Fertil Steril. 2018 02;109(2):213-220

Authors: Normand EA, Alaimo JT, Van den Veyver IB

Abstract
The advent of next-generation sequencing has enabled clinicians to assess many genes simultaneously and at high resolution. This is advantageous for diagnosing patients in whom a genetic disorder is suspected but who have a nonspecific or atypical phenotype or when the disorder has significant genetic heterogeneity. Herein, we describe common clinical applications of next-generation sequencing technology, as well as their respective benefits and limitations. We then discuss key considerations of variant interpretation and reporting, clinical utility, pre- and posttest genetic counseling, and ethical challenges. We will present these topics with an emphasis on their applicability to the reproductive medicine setting.

PMID: 29395096 [PubMed - indexed for MEDLINE]

Dysregulation of WTI (-KTS) is Associated with the Kidney-Specific Effects of the LMX1B R246Q Mutation.

Sci Rep. 2017 01 06;7:39933

Authors: Hall G, Lane B, Chryst-Ladd M, Wu G, Lin JJ, Qin X, Hauser ER, Gbadegesin R

Abstract
Mutations in the LIM homeobox transcription factor 1-beta (LMX1B) are a cause of nail patellar syndrome, a condition characterized by skeletal changes, glaucoma and focal segmental glomerulosclerosis. Recently, a missense mutation (R246Q) in LMX1B was reported as a cause of glomerular pathologies without extra-renal manifestations, otherwise known as nail patella-like renal disease (NPLRD). We have identified two additional NPLRD families with the R246Q mutation, though the mechanisms by which LMX1BR246Q causes a renal-specific phenotype is unknown. In this study, using human podocyte cell lines overexpressing either myc-LMX1BWT or myc-LMX1BR246Q, we observed dominant negative and haploinsufficiency effects of the mutation on the expression of podocyte genes such as NPHS1, GLEPP1, and WT1. Specifically, we observed a novel LMX1BR246Q-mediated downregulation of WT1(-KTS) isoforms in podocytes. In conclusion, we have shown that the renal-specific phenotype associated with the LMX1BR246Q mutation may be due to a dominant negative effect on WT1(-KTS) isoforms that may cause a disruption of the WT1 (-KTS):(+KTS) isoform ratio and a decrease in the expression of podocyte genes. Full delineation of the LMX1B gene regulon is needed to define its role in maintenance of glomerular filtration barrier integrity.

PMID: 28059119 [PubMed - indexed for MEDLINE]

Jaundice revisited: recent advances in the diagnosis and treatment of inherited cholestatic liver diseases.

J Biomed Sci. 2018 Oct 26;25(1):75

Authors: Chen HL, Wu SH, Hsu SH, Liou BY, Chen HL, Chang MH

Abstract
BACKGROUND: Jaundice is a common symptom of inherited or acquired liver diseases or a manifestation of diseases involving red blood cell metabolism. Recent progress has elucidated the molecular mechanisms of bile metabolism, hepatocellular transport, bile ductular development, intestinal bile salt reabsorption, and the regulation of bile acids homeostasis.
MAIN BODY: The major genetic diseases causing jaundice involve disturbances of bile flow. The insufficiency of bile salts in the intestines leads to fat malabsorption and fat-soluble vitamin deficiencies. Accumulation of excessive bile acids and aberrant metabolites results in hepatocellular injury and biliary cirrhosis. Progressive familial intrahepatic cholestasis (PFIC) is the prototype of genetic liver diseases manifesting jaundice in early childhood, progressive liver fibrosis/cirrhosis, and failure to thrive. The first three types of PFICs identified (PFIC1, PFIC2, and PFIC3) represent defects in FIC1 (ATP8B1), BSEP (ABCB11), or MDR3 (ABCB4). In the last 5 years, new genetic disorders, such as TJP2, FXR, and MYO5B defects, have been demonstrated to cause a similar PFIC phenotype. Inborn errors of bile acid metabolism also cause progressive cholestatic liver injuries. Prompt differential diagnosis is important because oral primary bile acid replacement may effectively reverse liver failure and restore liver functions. DCDC2 is a newly identified genetic disorder causing neonatal sclerosing cholangitis. Other cholestatic genetic disorders may have extra-hepatic manifestations, such as developmental disorders causing ductal plate malformation (Alagille syndrome, polycystic liver/kidney diseases), mitochondrial hepatopathy, and endocrine or chromosomal disorders. The diagnosis of genetic liver diseases has evolved from direct sequencing of a single gene to panel-based next generation sequencing. Whole exome sequencing and whole genome sequencing have been actively investigated in research and clinical studies. Current treatment modalities include medical treatment (ursodeoxycholic acid, cholic acid or chenodeoxycholic acid), surgery (partial biliary diversion and liver transplantation), symptomatic treatment for pruritus, and nutritional therapy. New drug development based on gene-specific treatments, such as apical sodium-dependent bile acid transporter (ASBT) inhibitor, for BSEP defects are underway.
SHORT CONCLUSION: Understanding the complex pathways of jaundice and cholestasis not only enhance insights into liver pathophysiology but also elucidate many causes of genetic liver diseases and promote the development of novel treatments.

PMID: 30367658 [PubMed - in process]

Exome sequencing in families with severe mental illness identifies novel and rare variants in genes implicated in Mendelian neuropsychiatric syndromes.

Psychiatry Clin Neurosci. 2018 Oct 27;:

Authors: Ganesh S, Ahmed P H, Nadella RK, More RP, Sheshadri M, Viswanath B, Rao M, Jain S, ADBS consortium, Mukherjee O

Abstract
AIM: Severe Mental Illnesses, such as bipolar disorder and schizophrenia, are highly heritable, and have a complex pattern of inheritance. Genome wide association studies detect a part of the heritability, which can be attributed to common genetic variation. Examination of rare variants with Next Generation Sequencing may add to the understanding of genetic architecture of SMIs.
METHODS: We analyzed 32 ill subjects from 8 multiplex families; and 33 healthy individuals by whole exome sequencing. Prioritized variants were selected by a 3-step filtering process, which included deleteriousness by 5 in silico algorithms; sharing within families by affected individuals, rarity in South Asian sample estimated using the Exome Aggregation Consortium data and complete absence of these variants in a control-individuals from the same gene pool.
RESULTS: We identified 42 rare, non-synonymous deleterious variants (~5 per pedigree) in this study. None of the variants were shared across families, indicating a 'private' mutational profile. Twenty (47.6%) of the variant harboring genes were previously reported to contribute to the risk of diverse neuropsychiatric syndromes; 9 (21.4%) of which were of Mendelian inheritance. These included genes carrying novel deleterious variants such as GRM1 gene implicated in Spinocerebellar ataxia 44 and NIPBL gene implicated in Cornelia de Lange syndrome.
CONCLUSION: NGS approaches in family-based studies are useful to identify novel and rare variants in genes for complex disorders like SMI. The findings of the study suggest a potential phenotypic burden of rare variants in Mendelian disease genes, indicating pleiotropic effects in the etiology of SMI. This article is protected by copyright. All rights reserved.

PMID: 30367527 [PubMed - as supplied by publisher]

Enabling genome-wide association testing with multiple diseases and no healthy controls.

Gene. 2018 Oct 23;:

Authors: Tom J, Chang D, Wuster A, Mukhyala K, Cuenco K, Cowgill A, Vogel J, Reeder J, Yaspan B, Hunkapiller J, Brauer M, Behrens T, Forrest W, Bhangale T

Abstract
MOTIVATION: While large-scale whole genome sequencing is feasible the high costs compel investigators to focus on disease subjects. As a result large sequencing datasets of samples with different diseases are often readily available, but not healthy controls to contrast them with. While it is possible to perform an association study using only diseases, the associations could be driven by a disease acting as a control and not the focal disease.
METHODS: We developed a genotype-on-phenotype reverse regression with a Bayesian spike and slab prior to enable association testing in datasets with multiple diseases. This method, referred to as revreg, flagged associations (both common and rare) that were driven by diseases that were not of primary interest.
RESULTS: Based on simulations, revreg had 80% power to detect an odds ratio of 1.74 for common variants (3500 samples total) and 3.73 for rare variants (14,000 samples total), with minimal type I error. For common variants, we tested this method on 3657 whole genome sequenced samples aimed at discovering variants associated with disease risk of Chronic Obstructive Pulmonary Disease using three other diseases as controls. We demonstrated detection of six highly significant associations likely due to Age-Related Macular Degeneration. In an exome dataset of 8836 samples aimed at characterizing rare variants associated with disease risk of Asthma, using five other diseases as controls, we detected and removed genic regions due to AMD (C3, CFH, CFHR5, CFI, and DNMT3A) and RA (KRTAP13-4).

PMID: 30366082 [PubMed - as supplied by publisher]

Determining the Quantitative Principles of T Cell Response to Antigenic Disparity in Stem Cell Transplantation.

Front Immunol. 2018;9:2284

Authors: Salman A, Koparde V, Hall CE, Jameson-Lee M, Roberts C, Serrano M, AbdulRazzaq B, Meier J, Kennedy C, Manjili MH, Spellman SR, Wijesinghe D, Hashmi S, Buck G, Qayyum R, Neale M, Reed J, Toor AA

Abstract
Alloreactivity compromising clinical outcomes in stem cell transplantation is observed despite HLA matching of donors and recipients. This has its origin in the variation between the exomes of the two, which provides the basis for minor histocompatibility antigens (mHA). The mHA presented on the HLA class I and II molecules and the ensuing T cell response to these antigens results in graft vs. host disease. In this paper, results of a whole exome sequencing study are presented, with resulting alloreactive polymorphic peptides and their HLA class I and HLA class II (DRB1) binding affinity quantified. Large libraries of potentially alloreactive recipient peptides binding both sets of molecules were identified, with HLA-DRB1 generally presenting a greater number of peptides. These results are used to develop a quantitative framework to understand the immunobiology of transplantation. A tensor-based approach is used to derive the equations needed to determine the alloreactive donor T cell response from the mHA-HLA binding affinity and protein expression data. This approach may be used in future studies to simulate the magnitude of expected donor T cell response and determine the risk for alloreactive complications in HLA matched or mismatched hematopoietic cell and solid organ transplantation.

PMID: 30364159 [PubMed - in process]

Common Variable Immunodeficiency with Genetic Defects Identified by Whole Exome Sequencing.

Biomed Res Int. 2018;2018:3724630

Authors: Li R, Zheng Y, Li Y, Zhang R, Wang F, Yang D, Ma Y, Mu X, Cao Z, Gao Z

Abstract
Common variable immunodeficiency (CVID) belongs to the primary immunodeficiency disorders (PIDs), presenting a profound heterogeneity in phenotype and genotype, with monogenic or complex causes. Recurrent respiratory infections are the most common clinical manifestations. CVID patients can also develop various autoimmune and lymphoproliferative complications. Genetic testing such as whole exome sequencing (WES) can be utilized to investigate likely genetic defects, helping for better clinical management. We described the clinical phenotypes of three sporadic cases of CVID, who developed recurrent respiratory infections with different autoimmune and lymphoproliferative complications. WES was applied to screen disease-causing or disease-associated mutations. Two patients were identified to have monogenic disorders, with compound heterozygous mutations in LRBA for one patient and a frameshift insertion in NFKB1 for another. The third patient was identified to be a complex form of CVID. Two novel mutations were identified, respectively, in LRBA and NFKB1. A combination of clinical and genetic diagnosis can be more extensively utilized in the clinical practice due to the complexity and heterogeneity of CVID.

PMID: 30363934 [PubMed - in process]

Moonlighting nuclear pore proteins: tissue-specific nucleoporin function in health and disease.

Histochem Cell Biol. 2018 Oct 25;:

Authors: Jühlen R, Fahrenkrog B

Abstract
The nuclear pore complex is the main transportation hub for exchange between the cytoplasm and the nucleus. It is built from nucleoporins that form distinct subcomplexes to establish this huge protein complex in the nuclear envelope. Malfunctioning of nucleoporins is well known in human malignancies, such as gene fusions of NUP214 and NUP98 in hematological neoplasms and overexpression of NUP88 in a variety of human cancers. In the past decade, the incremental utilization of next-generation sequencing has unraveled mutations in nucleoporin genes in the context of an increasing number of hereditary diseases, often in a tissue-specific manner. It emerges that, on one hand, the central nervous system and the heart are particularly sensitive to mutations in nucleoporin genes. On the other hand, nucleoporins forming the scaffold structure of the nuclear pore complex are eminently mutation-prone. These novel and exciting associations between nucleoporins and human diseases emphasize the need to shed light on these unanticipated tissue-specific roles of nucleoporins that may go well beyond their role in nucleocytoplasmic transport. In this review, the current insights into altered nucleoporin function associated with human hereditary disorders will be discussed.

PMID: 30361777 [PubMed - as supplied by publisher]

CRISPR-Cas9 human gene replacement and phenomic characterization in Caenorhabditis elegans to understand the functional conservation of human genes and decipher variants of uncertain significance.

Dis Model Mech. 2018 Oct 25;:

Authors: McDiarmid TA, Au V, Loewen AD, Liang J, Mizumoto K, Moerman DG, Rankin CH

Abstract
Our ability to sequence genomes has vastly surpassed our ability to interpret the genetic variation we discover. This presents a major challenge in the clinical setting, where the recent application of whole exome and whole genome sequencing has uncovered thousands of genetic variants of uncertain significance. Here, we present a strategy for targeted human gene replacement and phenomic characterization based on CRISPR-Cas9 genome engineering in the genetic model organism Caenorhabditis elegans that will facilitate assessment of the functional conservation of human genes and structure-function analysis of disease-associated variants with unprecedented precision. We validate our strategy by demonstrating that direct single-copy replacement of the C. elegans ortholog (daf-18) with the critical human disease-associated gene Phosphatase and Tensin Homolog (PTEN) is sufficient to rescue multiple phenotypic abnormalities caused by complete deletion of daf-18, including complex chemosensory and mechanosenory impairments. In addition, we used our strategy to generate animals harboring a single copy of the known pathogenic lipid phosphatase inactive PTEN variant (PTEN-G129E) and showed that our automated in vivo phenotypic assays could accurately and efficiently classify this missense variant as loss-of-function. The integrated nature of the human transgenes allows for analysis of both homozygous and heterozygous variants and greatly facilitates high-throughput precision medicine drug screens. By combining genome engineering with rapid and automated phenotypic characterization, our strategy streamlines identification of novel conserved gene functions in complex sensory and learning phenotypes that can be used as in vivo functional assays to decipher variants of uncertain significance.

PMID: 30361258 [PubMed - as supplied by publisher]

Familial amyloid polyneuropathy with chronic paroxysmal dry cough in Mainland China: A Chinese family with a proven heterozygous missense mutation c.349G>T in the transthyretin gene.

J Clin Neurosci. 2018 Oct 22;:

Authors: Yuan Z, Guo L, Liu X, Xiao X, Jiao B, Wang J, Yan X, Tang B, Shen L

Abstract
Familial amyloid polyneuropathy (FAP) is a rare autosomal dominant disorder characterized by amyloid accumulation in the peripheral nerves and other organs, including the heart, kidney, and eyes. So far, no case with FAP from Mainland China was reported with a heterozygous missense mutation c.349G>T in the Transthyretin (TTR) gene. We report a 58-year-old man presenting with progressive peripheral neuropathy, autonomic failure and chronic paroxysmal dry cough. His father, three elder brothers and an elder sister suffered from the similar symptoms. Diagnostic whole-exome sequencing revealed a proven heterozygous missense mutation c.349G>T in exon 4 of the TTR gene, resulting in replacement of alanine with serine at position 117 of the mature protein (Ala117Ser). This is the first FAP family with a proven missense mutation c.349G>T in Mainland China, as well as the first FAP case with chronic paroxysmal dry cough.

PMID: 30361054 [PubMed - as supplied by publisher]

Functional testing of a human PBX3 variant in zebrafish reveals a potential modifier role in congenital heart defects.

Dis Model Mech. 2018 Oct 18;11(10):

Authors: Farr GH, Imani K, Pouv D, Maves L

Abstract
Whole-genome and exome sequencing efforts are increasingly identifying candidate genetic variants associated with human disease. However, predicting and testing the pathogenicity of a genetic variant remains challenging. Genome editing allows for the rigorous functional testing of human genetic variants in animal models. Congenital heart defects (CHDs) are a prominent example of a human disorder with complex genetics. An inherited sequence variant in the human PBX3 gene (PBX3 p.A136V) has previously been shown to be enriched in a CHD patient cohort, indicating that the PBX3 p.A136V variant could be a modifier allele for CHDs. Pbx genes encode three-amino-acid loop extension (TALE)-class homeodomain-containing DNA-binding proteins with diverse roles in development and disease, and are required for heart development in mouse and zebrafish. Here, we used CRISPR-Cas9 genome editing to directly test whether this Pbx gene variant acts as a genetic modifier in zebrafish heart development. We used a single-stranded oligodeoxynucleotide to precisely introduce the human PBX3 p.A136V variant in the homologous zebrafish pbx4 gene (pbx4 p.A131V). We observed that zebrafish that are homozygous for pbx4 p.A131V are viable as adults. However, the pbx4 p.A131V variant enhances the embryonic cardiac morphogenesis phenotype caused by loss of the known cardiac specification factor, Hand2. Our study is the first example of using precision genome editing in zebrafish to demonstrate a function for a human disease-associated single nucleotide variant of unknown significance. Our work underscores the importance of testing the roles of inherited variants, not just de novo variants, as genetic modifiers of CHDs. Our study provides a novel approach toward advancing our understanding of the complex genetics of CHDs.

PMID: 30355621 [PubMed - in process]

Burden of rare variants in causative genes for amyotrophic lateral sclerosis (ALS) accelerates age at onset of ALS.

J Neurol Neurosurg Psychiatry. 2018 Oct 24;:

Authors: Naruse H, Ishiura H, Mitsui J, Takahashi Y, Matsukawa T, Tanaka M, Doi K, Yoshimura J, Morishita S, Goto J, Toda T, Tsuji S

Abstract
OBJECTIVES: To evaluate the burden of rare variants in the causative genes for amyotrophic lateral sclerosis (ALS) on the age at onset of ALS in a Japanese case series.
METHODS: We conducted whole-exome sequencing analysis of 89 families with familial ALS (FALS) and 410 patients with sporadic ALS (SALS) to identify known pathogenic mutations or rare functionally predicted deleterious variants in the causative genes for ALS. Rare variants (minor allele frequency <1%) with scaled Combined Annotation-Dependent Depletion score >20 were defined as rare functionally predicted deleterious variants. The patients with ALS were classified on the basis of the number of pathogenic and/or rare functionally predicted deleterious variants, and the age at onset was compared among the classified groups.
RESULTS: Whole-exome sequencing analysis revealed known pathogenic mutations or rare functionally predicted deleterious variants in causative genes for ALS in 56 families with FALS (62.9%) and 87 patients with SALS (21.2%). Such variants in multiple genes were identified in seven probands with FALS and eight patients with SALS. The ages at onset in the patients with ALS with multiple variants were significantly earlier than those in other patients with ALS. Even when the patients with known pathogenic mutations were excluded, a significantly earlier onset of the disease was still observed in patients with multiple rare functionally predicted deleterious variants.
CONCLUSIONS: A substantial number of patients carried rare variants in multiple genes, and the burden of rare variants in the known causative genes for ALS affects the age at onset in the Japanese ALS series.

PMID: 30355605 [PubMed - as supplied by publisher]

Driver mutations in Janus kinases in a mouse model of B-cell leukemia induced by deletion of PU.1 and Spi-B.

Blood Adv. 2018 Nov 13;2(21):2798-2810

Authors: Batista CR, Lim M, Laramée AS, Abu-Sardanah F, Xu LS, Hossain R, Bell GI, Hess DA, DeKoter RP

Abstract
Precursor B-cell acute lymphoblastic leukemia (B-ALL) is associated with recurrent mutations that occur in cancer-initiating cells. There is a need to understand how driver mutations influence clonal evolution of leukemia. The E26-transformation-specific (ETS) transcription factors PU.1 and Spi-B (encoded by Spi1 and Spib) execute a critical role in B-cell development and serve as complementary tumor suppressors. Here, we used a mouse model to conditionally delete Spi1 and Spib genes in developing B cells. These mice developed B-ALL with a median time to euthanasia of 18 weeks. We performed RNA and whole-exome sequencing (WES) on leukemias isolated from Mb1-CreΔPB mice and identified single nucleotide variants (SNVs) in Jak1, Jak3, and Ikzf3 genes, resulting in amino acid sequence changes. Jak3 mutations resulted in amino acid substitutions located in the pseudo-kinase (R653H, V670A) and in the kinase (T844M) domains. Introduction of Jak3 T844M into Spi1/Spib-deficient precursor B cells was sufficient to promote proliferation in response to low IL-7 concentrations in culture, and to promote proliferation and leukemia-like disease in transplanted mice. We conclude that mutations in Janus kinases represent secondary drivers of leukemogenesis that cooperate with Spi1/Spib deletion. This mouse model represents a useful tool to study clonal evolution in B-ALL.

PMID: 30355579 [PubMed - in process]

Healthcare Utilization and Patients' Perspectives After Receiving a Positive Genetic Test for Familial Hypercholesterolemia.

Circ Genom Precis Med. 2018 Aug;11(8):e002146

Authors: Jones LK, Kulchak Rahm A, Manickam K, Butry L, Lazzeri A, Corcoran T, Komar D, Josyula NS, Pendergrass SA, Sturm AC, Murray MF

Abstract
BACKGROUND: The MyCode Community Health Initiative (MyCode) is returning actionable results from whole exome sequencing. Familial hypercholesterolemia (FH) is an inherited condition characterized by premature cardiovascular disease.
METHODS: We used multiple methods to assess care in 28 MyCode participants who received FH results. Chart reviews were conducted on 23 individuals in the sample and 7 individuals participated semistructured interviews.
RESULTS: Chart reviews for 23 individuals with a Geisinger primary care provider found that 4 individuals (17% of 23) were at LDL-C (low-density lipoprotein cholesterol) goal (of either LDL-C <100 mg/dL for primary prevention and LDL-C <70 mg/dL for secondary prevention) and 17 individuals (74% of 23) were prescribed lipid-lowering therapy before genetic result disclosure. After disclosure of the genetic test result, 5 individuals (22% of 23) met their LDL-C goal and 18 individuals (78% of 23) were prescribed lipid-lowering therapy. Follow-up care about this result was not documented for 4 individuals (17% of 23). Changes to intensity of medication management were made for 8 individuals (47% of 17 individuals previously prescribed lipid-lowering therapy). Interviewed individuals (n=7) were not surprised by their result as all knew they had high cholesterol; however, individuals did not seem to discern FH as a separate condition from their high cholesterol.
CONCLUSIONS: Among individuals receiving genetic diagnosis of FH, >25% had no changes to lipid-lowering therapy, despite not being at LDL-C goal and learning their high cholesterol is related to a genetic condition requiring more aggressive treatment. Individuals and clinicians may have an inadequate understanding of FH as a distinct condition requiring enhanced medical management.

PMID: 30354341 [PubMed - in process]

Whole-Exome Sequencing Identifies Pathogenic Variants in TJP1 Gene Associated With Arrhythmogenic Cardiomyopathy.

Circ Genom Precis Med. 2018 Oct;11(10):e002123

Authors: De Bortoli M, Postma AV, Poloni G, Calore M, Minervini G, Mazzotti E, Rigato I, Ebert M, Lorenzon A, Vazza G, Cipriani A, Bariani R, Perazzolo Marra M, Husser D, Thiene G, Daliento L, Corrado D, Basso C, Tosatto SCE, Bauce B, van Tintelen JP, Rampazzo A

Abstract
BACKGROUND: Arrhythmogenic cardiomyopathy (ACM) is an inherited cardiac disease characterized by progressive fibro-fatty myocardial replacement, ventricular arrhythmia, heart failure, and sudden death. Causative mutations can be identified in 60% of patients, and most of them are found in genes encoding mechanical junction proteins of the intercalated disk.
METHODS: Whole-exome sequencing was performed on the proband of an ACM family. Sanger sequencing was used to screen for mutations the tight junction protein 1 ( TJP1) gene in unrelated patients. Predictions of local structure content and molecular dynamics simulations were performed to investigate the structural impact of the variants.
RESULTS: A novel c.2006A>G p.(Y669C) variant in TJP1 gene was identified by whole-exome sequencing in a patient with ACM. TJP1 encodes zonula occludens 1, an intercalated disk protein interacting with proteins of gap junctions and area composita. Additional rare TJP1 variants have been identified in 1 of 40 Italian probands (c.793C>T p.(R265W)) with arrhythmogenic right ventricular cardiomyopathy and in 2 of 43 Dutch/German patients (c. 986C>T, p.(S329L) and c.1079A>T, p.(D360V)) with dilated cardiomyopathy and recurrent ventricular tachycardia. The p.(D360V) variant was identified in a proband also carrying the p.(I156N) pathogenic variant in DSP. All 4 TJP1 variants are predicted to be deleterious and affect highly conserved amino acids, either at the GUK (guanylate kinase)-like domain (p.(Y669C)) or at the disordered region of the protein between the PDZ2 and PDZ3 domains (p.(R265W), p.(S329L), and p.(D360V)). The local unfolding induced by the former promotes structural rearrangements of the GUK domain, whereas the others are predicted to impair the function of the disordered region. Furthermore, rare variants in TJP1 are statistically enriched in patients with ACM relative to controls.
CONCLUSIONS: We provide here the first evidence linking likely pathogenic TJP1 variants to ACM. Prevalence and pathogenic mechanism of TJP1-mediated ACM remain to be determined.

PMID: 30354300 [PubMed - in process]

Loss-of-Function ABCC8 Mutations in Pulmonary Arterial Hypertension.

Circ Genom Precis Med. 2018 Oct;11(10):e002087

Authors: Bohnen MS, Ma L, Zhu N, Qi H, McClenaghan C, Gonzaga-Jauregui C, Dewey FE, Overton JD, Reid JG, Shuldiner AR, Baras A, Sampson KJ, Bleda M, Hadinnapola C, Haimel M, Bogaard HJ, Church C, Coghlan G, Corris PA, Eyries M, Gibbs JSR, Girerd B, Houweling AC, Humbert M, Guignabert C, Kiely DG, Lawrie A, MacKenzie Ross RV, Martin JM, Montani D, Peacock AJ, Pepke-Zaba J, Soubrier F, Suntharalingam J, Toshner M, Treacy CM, Trembath RC, Vonk Noordegraaf A, Wharton J, Wilkins MR, Wort SJ, Yates K, Gräf S, Morrell NW, Krishnan U, Rosenzweig EB, Shen Y, Nichols CG, Kass RS, Chung WK

Abstract
BACKGROUND: In pulmonary arterial hypertension (PAH), pathological changes in pulmonary arterioles progressively raise pulmonary artery pressure and increase pulmonary vascular resistance, leading to right heart failure and high mortality rates. Recently, the first potassium channelopathy in PAH, because of mutations in KCNK3, was identified as a genetic cause and pharmacological target.
METHODS: Exome sequencing was performed to identify novel genes in a cohort of 99 pediatric and 134 adult-onset group I PAH patients. Novel rare variants in the gene identified were independently identified in a cohort of 680 adult-onset patients. Variants were expressed in COS cells and function assessed by patch-clamp and rubidium flux analysis.
RESULTS: We identified a de novo novel heterozygous predicted deleterious missense variant c.G2873A (p.R958H) in ABCC8 in a child with idiopathic PAH. We then evaluated all individuals in the original and a second cohort for rare or novel variants in ABCC8 and identified 11 additional heterozygous predicted damaging ABCC8 variants. ABCC8 encodes SUR1 (sulfonylurea receptor 1)-a regulatory subunit of the ATP-sensitive potassium channel. We observed loss of ATP-sensitive potassium channel function for all ABCC8 variants evaluated and pharmacological rescue of all channel currents in vitro by the SUR1 activator, diazoxide.
CONCLUSIONS: Novel and rare missense variants in ABCC8 are associated with PAH. Identified ABCC8 mutations decreased ATP-sensitive potassium channel function, which was pharmacologically recovered.

PMID: 30354297 [PubMed - in process]

Allele balance bias identifies systematic genotyping errors and false disease associations.

Hum Mutat. 2018 Oct 24;:

Authors: Muyas F, Bosio M, Puig A, Susak H, Domènech-Salgado L, Escaramis G, Zapata L, Demidov G, Estivill X, Rabionet R, Ossowski S

Abstract
In recent years, Next Generation Sequencing (NGS) has become a cornerstone of clinical genetics and diagnostics. Many clinical applications require high precision, especially if rare events such as somatic mutations in cancer or genetic variants causing rare diseases need to be identified. Although random sequencing errors can be modeled statistically and deep sequencing minimizes their impact, systematic errors remain a problem even at high depth of coverage. Understanding their source is crucial to increase precision of clinical NGS applications. In this work, we studied the relation between recurrent biases in allele balance (AB), systematic errors and false positive variant calls across a large cohort of human samples analyzed by whole exome sequencing (WES). We have modeled the allele balance distribution for biallelic genotypes in 987 WES samples in order to identify positions recurrently deviating significantly from the expectation, a phenomenon we termed allele balance bias (ABB). Furthermore, we have developed a genotype callability score based on ABB for all positions of the human exome, which detects false positive variant calls that passed state-of-the-art filters. Finally, we demonstrate the use of ABB for detection of false associations proposed by rare variant association studies (RVAS). Availability: https://github.com/Francesc-Muyas/ABB. This article is protected by copyright. All rights reserved.

PMID: 30353964 [PubMed - as supplied by publisher]