American College of Medical Genetics guideline on the cytogenetic evaluation of the individual with developmental delay or mental retardation

Neurodevelopmental defects in a mouse model of O-GlcNAc transferase intellectual disability

The addition of O-linked β-N-acetylglucosamine (O-GlcNAc) to proteins (referred to as O-GlcNAcylation) is a modification that is crucial for vertebrate development. O-GlcNAcylation is catalyzed by O-GlcNAc transferase (OGT) and reversed by O-GlcNAcase (OGA). Missense variants of OGT have recently been shown to segregate with an X-linked syndromic form of intellectual disability, OGT-linked congenital disorder of glycosylation (OGT-CDG). Although the existence of OGT-CDG suggests that O-GlcNAcylation is crucial for neurodevelopment and/or cognitive function, the underlying pathophysiologic mechanisms remain unknown. Here we report a mouse line that carries a catalytically impaired OGT-CDG variant. These mice show altered O-GlcNAc homeostasis with decreased global O-GlcNAcylation and reduced levels of OGT and OGA in the brain. Phenotypic characterization of the mice revealed lower body weight associated with reduced body fat mass, short stature and microcephaly. This mouse model will serve as an important tool to study genotype-phenotype correlations in OGT-CDG in vivo and for the development of possible treatment avenues for this disorder.

Novel SETBP1 mutation in a chinese family with intellectual disability

BACKGROUND

Intellectual disability (ID) is characterized by an IQ < 70, which implies below-average intellectual function and a lack of skills necessary for daily living. ID may occur due to multiple causes, such as metabolic, infectious, and chromosomal causes. ID affects approximately 1-3% of the population; however, the cause can be identified in only 25% of clinical patients.

METHODS

To find the cause of genetic ID in a family, we performed whole-exome sequencing and Sanger sequencing to confirm the presence of a SETBP1 variant and real-time quantitative polymerase chain reaction to detect SETBP1 expression in the proband and normal controls.

RESULTS

A novel variant, c.942_943insGT (p. Asp316TrpfsTer28), was found in SETBP1. Furthermore, we observed that SETBP1 expression in patients was only 20% that of normal controls (P < 0.05).

CONCLUSION

A heterozygous variant in SETBP1 associated with ID was found. This report provides further evidence for its genetic basis and support for clinical genetic diagnosis.

Chromosomal Aberrations in Pediatric Patients With Moderate/Severe Developmental Delay/Intellectual Disability With Abundant Phenotypic Heterogeneities: A Single-Center Study

BACKGROUND

This study aimed to examine the clinical usefulness of chromosome microarray (CMA) for selective implementation in patients with unexplained moderate or severe developmental delay/intellectual disability (DD/ID) and/or combined with different dysphonic features in the Han Chinese population.

METHODS

We retrospectively analyzed data on 122 pediatric patients with unexplained isolated moderate/severe DD/ID with or without autism spectrum disorders, epilepsy, dystonia, and congenital abnormalities from a single-center neurorehabilitation clinic in southern China.

RESULTS

A total of 46 probands (37.7%) had abnormal CMA results among the 122 study patients. With the exclusion of aneuploidies, uniparental disomies, and multiple homozygotes, 37 patients harbored 39 pathogenic copy number variations (pCNVs) (median [interquartile range] size: 3.57 [1.6 to 7.1] Mb; 33 deletions and 6 duplications), enriched in chromosomes 5, 7, 15, 17, and 22, with a markedly high prevalence of Angelman/Prader-Willi syndrome (24.3% [nine of 37]). Three rare deletions in the regions 5q33.2q34, 17p13.2, and 13q33.2 were reported, with specific delineation of clinical phenotypes. The frequencies of pCNVs were 18%, 33.3%, 38.89%, 41.67%, and 100% for patients with 1, 2, 3, 4, and 5 study phenotypes, respectively; patients with more concomitant abnormalities in the heart, brain, craniofacial region, and/or other organs had a higher CMA diagnostic yield and pCNV prevalence (P < 0.05).

CONCLUSIONS

Clinical application of CMA as a first-tier test among patients with moderate/severe DD/ID combined with congenital structural anomalies improved diagnostic yields and the quality of clinical management in this series of patients.

Knowledge, attitudes and experiences of genetic testing for autism spectrum disorders among caregivers, patients, and health providers: A systematic review

BACKGROUND

Several genetic testing techniques have been recommended as a first-tier diagnostic tool in clinical practice for diagnosing autism spectrum disorder (ASD). However, the actual usage rate varies dramatically. This is due to various reasons, including knowledge and attitudes of caregivers, patients, and health providers toward genetic testing. Several studies have therefore been conducted worldwide to investigate the knowledge, experiences, and attitudes toward genetic testing among caregivers of children with ASD, adolescent and adult ASD patients, and health providers who provide medical services for them. However, no systematic review has been done.

AIM

To systematically review research on knowledge, experiences, and attitudes towards genetic testing among caregivers of children with ASD, adolescent and adult ASD patients, and health providers.

METHODS

We followed the Preferred Reporting Items for Systematic Reviews and Meta-analyses guidelines and searched the literature in three English language databases (PubMed, Web of Science, and PsychInfo) and two Chinese databases (CNKI and Wanfang). Searched literature was screened independently by two reviewers and discussed when inconsistency existed. Information on characteristics of the study, characteristics of participants, and main findings regarding knowledge, experience, and attitudes of caregivers of children with ASD, adolescent and adult ASD patients, and health providers concerning ASD genetic testing were extracted from included papers into a charting form for analysis.

RESULTS

We included 30 studies published between 2012 and 2022 and conducted in 9 countries. Most of the studies (n = 29) investigated caregivers of children with ASD, one study also included adolescent and adult patients, and two covered health providers. Most (51.0%-100%) of the caregivers/patients knew there was a genetic cause for ASD and 17.0% to 78.1% were aware of ASD genetic testing. However, they lacked full understanding of genetic testing. They acquired relevant and necessary information from physicians, the internet, ASD organizations, and other caregivers. Between 9.1% to 72.7% of caregivers in different studies were referred for genetic testing, and between 17.4% to 61.7% actually obtained genetic testing. Most caregivers agreed there are potential benefits following genetic testing, including benefits for children, families, and others. However, two studies compared perceived pre-test and post-test benefits with conflicting findings. Caregivers concerns included high costs, unhelpful results, negative influences (e.g., causing family conflicts, causing stress/risk/pain to children etc.) prevented some caregivers from using genetic testing. Nevertheless, 46.7% to 95.0% caregivers without previous genetic testing experience intended to obtain it in the future, and 50.5% to 59.6% of parents previously obtaining genetic testing would recommend it to other parents. In a single study of child and adolescent psychiatrists, 54.9% of respondents had ordered ASD genetic testing for their patients in the prior 12 mo, which was associated with greater knowledge of genetic testing.

CONCLUSION

Most caregivers are willing to learn about and use genetic testing. However, the review showed their current knowledge is limited and usage rates varied widely in different studies.

Prenatal genetic analysis of fetal aberrant right subclavian artery with or without additional ultrasound anomalies in a third level referral center

To evaluate the correlation between chromosomal abnormalities and fetal aberrant right subclavian artery (ARSA) with or without additional ultrasound anomalies (UAs). A total of 340 fetuses diagnosed with ARSA by ultrasound between December, 2015, and July, 2021, were included. All cases were subdivided into three groups: (A) 121 (35.6%) cases with isolated ARSA, (B) 91 (26.8%) cases with soft markers, and (C) 128 (37.6%) cases complicated with other UAs. Invasive testing was performed via amniotic fluid or cord blood karyotyping and chromosomal microarray analysis (CMA) in parallel, and pregnancy outcomes were followed. Karyotype abnormalities were identified in 18/340 (5.3%) patients. Karyotype abnormalities in Groups A, B, and C were 0/121 (0.0%), 7/91 (7.7%), and 11/128 (8.6%), respectively. CMA abnormalities with clinically significant variants were detected in 37/340 (10.9%) cases, of which 22q11.2 deletion syndrome and trisomy 21 accounted for 48.6% (18/37). The overall abnormal CMA with clinically significant variant detection rates in Groups A, B, and C were 3/121(2.5%), 13/91 (14.3%), and 21/128 (16.4%), respectively. There were significant difference in clinically significant CMA anomalies detection rate between Groups A and C (p < 0.05), as well as Groups A and B (p < 0.05). Comparing CMA to karyotyping showed a clinically significant incremental yield in Group C (7.8%, 10/128) compared to Groups A (2.5%, 3/121) and B (6.6%, 6/91) (p > 0.05). Fetal ARSA with additional UAs, concurred with cardiac and extra-cardiac anomalies, constitutes a high-risk factor for chromosomal aberrations, especially for pathogenic or likely pathogenic copy number variants.

Utility of whole-exome sequencing for patients with multiple congenital anomalies with or without intellectual disability/developmental delay in East Asia population

BACKGROUND

Congenital anomalies (CAs) with or without intellectual disability (ID)/developmental delay (DD) comprise a heterogeneous spectrum of diseases that affect approximately 3% of live births worldwide. Recently, whole-exome sequencing (WES) demonstrated the highly heterogeneous genetic causes of CAs. The purpose of this study was to evaluate a referral system to increase the yield of WES for CAs.

METHODS

From August 2018 to July 2019, patients with CAs, with or without ID/DD, after excluding gross chromosomal aberrations, were referred to geneticists in two medical centers. Variant prioritization was conducted with an AI-assisted tool for whole exomes or a CA-related gene panel.

RESULTS

Forty patients (27 males and 13 females) with CAs were enrolled in the study with a mean age of 4.71 years (range, 0.01-18.2). Pathogenic variants in 14 genes were discovered in 16 patients (three patients with CHD7 and 13 patients with one gene each of ATP6V1B2, TAF6, COL4A3BP, ANKH, BMP2, SMARCA4, CUL4B, PGAP3, SOX11, FBN2, PTPN11, SOS1, or PROKR2), with a positive diagnostic rate of 40%. Among the 16 positive cases, 13 (81%) also had ID/DD. The inheritance was autosomal dominant in 13 (81%), autosomal recessive in two (13%), and X-linked in one (6%). Only five patients received a correct clinical diagnosis before WES. The analyses of patients with a negative genetic diagnosis revealed a phenotype and gene mutation load similar to those of the positive-finding patients but with a lower percentage of ID/DD.

CONCLUSIONS

The careful selection of patients by experienced geneticists and the exclusion of chromosomal aberrations raises the positive rate of the molecular diagnosis for CAs to 40%. However, more than half of the patients with CAs still do not have a genetic diagnosis by current technologies.

Identifying Genetic Etiology in Patients with Intellectual Disability: An Experience in Public Health Services in Northeastern Brazil

Intellectual disability (ID) is considered a common neuropsychiatric disorder that affects up to 3% of the population. The etiologic origin of ID may be genetic, environmental, and multifactorial. Chromosomopathies are relatively common among the genetic causes of ID, especially in the most severe cases and those associated with dysmorphic features. Currently, the application of new molecular cytogenetics technologies has increasingly allowed the identification of microdeletions, microduplications, and unbalanced translocations as causes of ID. The objective of this study was to investigate the etiology of ID in patients admitted to a public hospital in Northeastern Brazil. In total, 119 patients with ID who had normal karyotypes and fragile X exams participated in this study. The patients were initially physically examined for microdeletion syndromes and then tested using fluorescence in situ hybridization (FISH), multiplex ligation-dependent probe amplification (MLPA), methylation-sensitive polymerase chain reaction (MS-PCR), and chromosome microarray analysis (CMA), according to clinical suspicion. Patients with no diagnoses after FISH, MLPA, and/or MS-PCR evaluations were subsequently tested by CMA. The rate of etiologic diagnoses of ID in the current study was 28%. FISH diagnosed 25 out of 79 tested (31%), MLPA diagnosed 26 out of 79 tested (32%), MS-PCR diagnosed 7 out of 20 tested (35%), and the single nucleotide polymorphism array diagnosed 6 out of 27 tested (22%). Although the CMA is the most complete and recommended tool for the diagnosis of microdeletions, microduplications, and unbalance translocations in patients with ID, FISH, MLPA, and MS-PCR testing can be used as the first tests for specific syndromes, as long as the patients are first physically screened clinically, especially in the public health networks system in Brazil, where resources are scarce.

Novel Synonymous and Frameshift Variants in the TRIP12 Gene Identified in 2 Chinese Patients With Intellectual Disability

Background and Objectives

Clark-Baraitser syndrome is characterized by intellectual disability with or without autism spectrum disorders, speech delay, motor delay, behavioral abnormalities, and facial dysmorphism. It is caused by a heterozygous pathogenic variant in the thyroid hormone receptor interactor 12 (TRIP12) gene. However, loss of function and haploinsufficiency are the pathogenic mechanisms behind the TRIP12-related disorder.

Methods

We conducted an exome sequencing analysis for 2 unrelated patients with moderate intellectual disability, speech delay, and motor delay.

Results

We identified 2 de novo TRIP12 mutations in these 2 patients. One patient had a frameshift duplication, whereas the other had a synonymous variant. Both patients presented with common features of the syndrome, but clinical heterogeneity has been also observed between them. For the synonymous variant, reverse transcription PCR in RNA extracted from leukocytes demonstrated the presence of a truncated messenger RNA (mRNA) transcript that skipped exon 12. This transcript escapes degradation at the mRNA level. To assess the effect of the synonymous substitute on TRIP12 proteolytic activity, the expression of 9 known responsive genes at the mRNA level was measured, of which 3 genes were upregulated at least 2-fold in the patient.

Discussion

We reported 2 patients with Clark-Baraitser syndrome caused by novel synonymous and frameshift variants in the TRIP12 gene, and our study expands the mutation spectrum of the TRIP12 gene. This study will help to improve our understanding of variable phenotypic presentations in TRIP12-related disorders.

Underlying genetic etiologies of congenital diaphragmatic hernia

Congenital diaphragmatic hernia (CDH) is often detectable prenatally. Advances in genetic testing have made it possible to obtain a molecular diagnosis in many fetuses with CDH. Here, we review the aneuploidies, copy number variants (CNVs), and single genes that have been clearly associated with CDH. We suggest that array-based CNV analysis, with or without a chromosome analysis, is the optimal test for identifying chromosomal abnormalities and CNVs in fetuses with CDH. To identify causative sequence variants, whole exome sequencing (WES) is the most comprehensive strategy currently available. Whole genome sequencing (WGS) with CNV analysis has the potential to become the most efficient and effective means of identifying an underlying diagnosis but is not yet routinely available for prenatal diagnosis. We describe how to overcome and address the diagnostic and clinical uncertainty that may remain after genetic testing, and review how a molecular diagnosis may impact recurrence risk estimations, mortality rates, and the availability and outcomes of fetal therapy. We conclude that after the prenatal detection of CDH, patients should be counseled about the possible genetic causes of the CDH, and the genetic testing modalities available to them, in accordance with generally accepted guidelines for pretest counseling in the prenatal setting.

The diagnostic trajectory of infants and children with clinical features of genetic disease

We characterized US pediatric patients with clinical indicators of genetic diseases, focusing on the burden of disease, utilization of genetic testing, and cost of care. Curated lists of diagnosis, procedure, and billing codes were used to identify patients with clinical indicators of genetic disease in healthcare claims from Optum's de-identified Clinformatics® Database (13,076,038 unique patients). Distinct cohorts were defined to represent permissive and conservative estimates of the number of patients. Clinical phenotypes suggestive of genetic diseases were observed in up to 9.4% of pediatric patients and up to 44.7% of critically-ill infants. Compared with controls, patients with indicators of genetic diseases had higher utilization of services (e.g., mean NICU length of stay of 31.6d in a cohort defined by multiple congenital anomalies or neurological presentations compared with 10.1d for patients in the control population (P < 0.001)) and higher overall costs. Very few patients received any genetic testing (4.2-8.4% depending on cohort criteria). These results highlight the substantial proportion of the population with clinical features associated with genetic disorders and underutilization of genetic testing in these populations.

A rare familial rearrangement of chromosomes 9 and 15 associated with intellectual disability: a clinical and molecular study

Background

There are many reports on rearrangements occurring separately in the regions of chromosomes 9p and 15q affected in the case under study. 15q duplication syndrome is caused by the presence of at least one extra maternally derived copy of the Prader–Willi/Angelman critical region. Trisomy 9p is the fourth most frequent chromosome anomaly with a clinically recognizable syndrome often accompanied by intellectual disability. Here we report a new case of a patient with maternally derived unique complex sSMC resulting in partial trisomy of both chromosomes 9 and 15 associated with intellectual disability.

Case presentation

We characterise a supernumerary derivative chromosome 15: 47,XY,+der(15)t(9;15)(p21.2;q13.2), likely resulting from 3:1 malsegregation during maternal gametogenesis. Chromosomal analysis showed that a phenotypically normal mother is a carrier of balanced translocation t(9;15)(p21.1;q13.2). Her 7-year-old son showed signs of intellectual disability and a number of physical abnormalities including bilateral cryptorchidism and congenital megaureter. The child’s magnetic resonance imaging showed changes in brain volume and in structural and functional connectivity revealing phenotypic changes caused by the presence of the extra chromosome material, whereas the mother’s brain MRI was normal. Sequence analyses of the microdissected der(15) chromosome detected two breakpoint regions: HSA9:25,928,021-26,157,441 (9p21.2 band) and HSA15:30,552,104-30,765,905 (15q13.2 band). The breakpoint region on chromosome HSA9 is poor in genetic features with several areas of high homology with the breakpoint region on chromosome 15. The breakpoint region on HSA15 is located in the area of a large segmental duplication.

Conclusions

We discuss the case of these phenotypic and brain MRI features in light of reported signatures for 9p partial trisomy and 15 duplication syndromes and analyze how the genomic characteristics of the found breakpoint regions have contributed to the origin of the derivative chromosome. We recommend MRI for all patients with a developmental delay, especially in cases with identified rearrangements, to accumulate more information on brain phenotypes related to chromosomal syndromes.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13039-021-00565-y.

An ethical analysis of divergent clinical approaches to the application of genetic testing for autism and schizophrenia

Genetic testing to identify genetic syndromes and copy number variants (CNVs) via whole genome platforms such as chromosome microarray (CMA) or exome sequencing (ES) is routinely performed clinically, and is considered by a variety of organizations and societies to be a "first-tier" test for individuals with developmental delay (DD), intellectual disability (ID), or autism spectrum disorder (ASD). However, in the context of schizophrenia, though CNVs can have a large effect on risk, genetic testing is not typically a part of routine clinical care, and no clinical practice guidelines recommend testing. This raises the question of whether CNV testing should be similarly performed for individuals with schizophrenia. Here we consider this proposition in light of the history of genetic testing for ID/DD and ASD, and through the application of an ethical analysis designed to enable robust, accountable and justifiable decision-making. Using a systematic framework and application of relevant bioethical principles (beneficence, non-maleficence, autonomy, and justice), our examination highlights that while CNV testing for the indication of ID has considerable benefits, there is currently insufficient evidence to suggest that overall, the potential harms are outweighed by the potential benefits of CNV testing for the sole indications of schizophrenia or ASD. However, although the application of CNV tests for children with ASD or schizophrenia without ID/DD is, strictly speaking, off-label use, there may be clinical utility and benefits substantive enough to outweigh the harms. Research is needed to clarify the harms and benefits of testing in pediatric and adult contexts. Given that genetic counseling has demonstrated benefits for schizophrenia, and has the potential to mitigate many of the potential harms from genetic testing, any decisions to implement genetic testing for schizophrenia should involve high-quality evidence-based genetic counseling.

Inherited unbalanced translocation (4p16.3p15.32 duplication/8p23.3p23.2deletion) in the four generation pedigree with intellectual disability/developmental delay

Chromosomal copy number variants (CNVs) are an important cause of congenital malformations and mental retardation. This study reported a large Chinese pedigree (4-generation, 76 members) with mental retardation caused by chromosome microduplication/microdeletion. There were 10 affected individuals with intellectual disability (ID), developmental delay (DD), and language delay phenotypes. SNP array analysis was performed in the proband and eight patients and found all of them had a microduplication of chromosome 4p16.3p15.2 and a microdeletion of chromosome 8p23.3p23.2. The high-resolution karyotyping analysis of the proband had unbalanced karyotype [46, XY, der(8)t(4;8)(p15.2;p23.1)mat], his mother had balanced karyotype [46, XX, t(4;8) (p15.2;p23.1)], whereas his father had normal karyotype [46,XY]. Fluorescence in situ hybridization (FISH) analysis further confirmed that the proband’s mother had a balanced translocation between the short arm terminal segment of chromosome 4 and the short arm end segment of chromosome 8, ish t(4;8)(8p + ,4q + ;4p + ,8q +). In conclusion, all the patients inherited chromosomes 8 with 4p16.3p15.2 duplication and 8p23.3p23.2 deletion from their parental balanced translocation, which might be the cause of the prevalence of intellectual disability. Meanwhile, 8p23.3p23.2 deletion, rather than 4p16.3p15.2 duplication might cause a more severe clinical syndrome.

The introduction of clinical genetic testing in Ethiopia: Experiences and lessons learned

Limited data are available on genetic testing laboratories in low- and middle-income countries including those in sub-Saharan Africa (SSA). To characterize the need for genetic testing in SSA we describe the experience of MRC-ET Advanced Laboratory, a genetic testing laboratory in Ethiopia. Test results were analyzed based on indication(s) for testing, referral category, and diagnostic yield. A total of 1311 tests were run using the full MRC-Holland catalogue of Multiplex-Ligation Probe Amplification assays. Of all samples, 77% were postnatal samples, 15% products of conception (POC), and 8% amniotic samples. Of postnatal samples, the most common testing categories were multiple congenital anomalies (32%), disorders of sex development (17%), and Obstetrics/Gynecology (16%). Forty-three percent of postnatal samples were diagnostic, 11% were variants of uncertain significance (VUS), and 46% were normal with Trisomy 21 the most common diagnosis. Of POC samples, 10% were diagnostic, 34% revealed VUSs, and 55% were normal with Trisomy 18 the most common diagnosis. Of amniotic samples 17.5% were diagnostic, 3% revealed VUSs, and 79% were normal with Trisomy 18 the most common diagnosis. There is increasing demand for genetic testing in Ethiopia. Diagnostic genetic testing in SSA deserves increased attention as testing platforms become more affordable.

Laboratory testing for fragile X, 2021 revision: a technical standard of the American College of Medical Genetics and Genomics (ACMG)

Molecular genetic testing of the FMR1 gene is commonly performed in clinical laboratories. Pathogenic variants in the FMR1 gene are associated with fragile X syndrome, fragile X-associated tremor ataxia syndrome (FXTAS), and fragile X-associated primary ovarian insufficiency (FXPOI). This document provides updated information regarding FMR1 pathogenic variants, including prevalence, genotype-phenotype correlations, and variant nomenclature. Methodological considerations are provided for Southern blot analysis and polymerase chain reaction (PCR) amplification of FMR1, including triplet repeat-primed and methylation-specific PCR.The American College of Medical Genetics and Genomics (ACMG) Laboratory Quality Assurance Committee has the mission of maintaining high technical standards for the performance and interpretation of genetic tests. In part, this is accomplished by the publication of the document ACMG Technical Standards for Clinical Genetics Laboratories, which is now maintained online ( http://www.acmg.net ). This subcommittee also reviews the outcome of national proficiency testing in the genetics area and may choose to focus on specific diseases or methodologies in response to those results. Accordingly, the subcommittee selected fragile X syndrome to be the first topic in a series of supplemental sections, recognizing that it is one of the most frequently ordered genetic tests and that it has many alternative methods with different strengths and weaknesses. This document is the fourth update to the original standards and guidelines for fragile X testing that were published in 2001, with revisions in 2005 and 2013, respectively.This versionClarifies the clinical features associated with different FMRI variants (Section 2.3)Discusses important reporting considerations (Section 3.3.1.3)Provides updates on technology (Section 4.1).

About classical molecular genetics, cytogenetic and molecular cytogenetic data not considered by Genome Reference Consortium and thus not included in genome browsers like UCSC, Ensembl or NCBI

Background

The Genome Reference Consortium (GRC) has according to its own statement the “mission to improve the human reference genome assembly, correcting errors and adding sequence to ensure it provides the best representation of the human genome to meet basic and clinical research needs”. Data from GRC is included in genome browsers like UCSC (University of California, Santa Cruz), Ensembl or NCBI (National Center for Biotechnology Information) and are thereby bases for scientific and diagnostically working human genetic community.

Method

Here long standing knowledge deriving from classical molecular genetic, cytogenetic and molecular cytogenetic data, not being considered yet by GRC was revisited.

Results

There were three major points identified: (1) GRC missed to including three chromosomal subbands, each, for 1q32.1, 2p21, 5q13.2, 6p22.3 and 6q21, which were defined by International System for Human Cytogenetic Nomenclature (ISCN) already back in 1980s; instead GRC included additional 6 subbands not ever recognized by ISCN. (2) GRC defined 34 chromosomal subbands of 0.1 to 0.9 Mb in size, while it is general agreement of cytogeneticists that it unlikely to detect chromosomal aberrations below 1–2 Mb in size by GTG-banding. And (3): still all sequences used in molecular cytogenetic routine diagnostics to detect heterochromatic and/ or pericentromeric satellite DNA sequences within the human genome are not included yet into human reference genome. For those sequences, localization and approximate sizes have been determined in the 1970s to 1990, and if included at least ~ 100 Mb of the human genome sequence could be added to the genome browsers.

Conclusion

Overall, taking into account the here mentioned points and correcting and including the data will definitely provide to the still not being completely finished mapping of the human genome.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13039-021-00540-7.

Loss of O-GlcNAcase catalytic activity leads to defects in mouse embryogenesis

O-GlcNAcylation is an essential post-translational modification that has been implicated in neurodevelopmental and neurodegenerative disorders. O-GlcNAcase (OGA), the sole enzyme catalyzing the removal of O-GlcNAc from proteins, has emerged as a potential drug target. OGA consists of an N-terminal OGA catalytic domain and a C-terminal pseudo histone acetyltransferase (HAT) domain with unknown function. To investigate phenotypes specific to loss of OGA catalytic activity and dissect the role of the HAT domain, we generated a constitutive knock-in mouse line, carrying a mutation of a catalytic aspartic acid to alanine. These mice showed perinatal lethality and abnormal embryonic growth with skewed Mendelian ratios after day E18.5. We observed tissue-specific changes in O-GlcNAc homeostasis regulation to compensate for loss of OGA activity. Using X-ray microcomputed tomography on late gestation embryos, we identified defects in the kidney, brain, liver, and stomach. Taken together, our data suggest that developmental defects during gestation may arise upon prolonged OGA inhibition specifically because of loss of OGA catalytic activity and independent of the function of the HAT domain.

Triple diagnosis of Wiedemann-Steiner, Waardenburg and DLG3-related intellectual disability association found by WES: A case report

BACKGROUND

The development of whole-exome sequencing (WES) and whole-genome sequencing (WGS) for clinical purposes now allows the identification of multiple pathogenic variants in patients with a rare disease. This occurs even when a single causative gene was initially suspected. We report the case of an 8-year-old patient with global developmental delays and dysmorphic features, with a possibly pathogenic variant in three distinct genes.

METHODS

Trio-based exome sequencing was performed by IntegraGen SA (Evry, France), on an Illumina HiSeq4000 (Illumina, San Diego, CA, USA). Sanger sequencing was performed to confirm the variants that were found.

RESULTS

WES showed the presence of three possibly deleterious variants: KMT2A: c.9068delA;p.Gln3023Argfs*3 de novo, PAX3: c.530C>G;p.Ala177Gly de novo and DLG3: c.127delG;p.Asp43Metfs*22 hemizygous inherited from the mother. KMT2A pathogenic variants are involved in Wiedemann-Steiner syndrome, and PAX3 is the gene responsible for Waardenburg syndrome. DLG3 variants have been described in a non-syndromic X-related intellectual disability.

CONCLUSIONS

Considering the dysmorphic features and intellectual disability presented by this patient, these three variants were imputed as pathogenic and their association was considered responsible for his phenotype. Dual molecular diagnoses have already been found by WES in several cohorts with an average of diagnostic yield of 7%. This case demonstrates and reminds us of the importance of analyzing exomes rigorously and exhaustively because, in some cases (< 10%), it can explain superimposed traits or blended phenotypes.

Methodological quality of clinical practice guidelines for genetic testing in children: A systematic assessment using the appraisal of guidelines for research and evaluation II instrument

Genetic testing of children is faced with numerous problems. High-quality clinical practice guidelines (CPGs) are needed to ensure its safe, and appropriate use. This study aimed to systematically identify the current CPGs for genetic testing in children, and to assess the methodological quality of these CPGs.We searched 6 databases, 3 guideline clearinghouses, and 9 web sites of relevant academic agencies from inception to February 2019. CPGs focused on genetic testing in children were included. Four reviewers independently appraised the quality of the eligible CPGs using the appraisal of guidelines for research, and evaluation (AGREE) II instrument.Seventeen CPGs meeting our inclusion criteria were included. Among them, 16 CPGs were focused on the genetic diagnosis/evaluation of diseases, while only 1 CPG was focused on pharmacogenetics. The median domain scores from highest to lowest were: scope and purpose 80.56% (range: 56.95%-87.50%), clarity of presentation 72.22% (range: 45.83%-88.89%), stakeholder involvement 45.83% (range: 27.78%-55.56%), applicability 31.25% (range: 19.79%-54.17%), rigor of development 21.88%, (range: 13.02%-71.88%), and editorial independence 18.75% (range: 0%-83.33%). According to the overall quality, 6 (35%) CPGs were "not recommended," 8 (47%) CPGs were "recommended with modifications," and only 3 (18%) CPGs were "recommended." The clinical topics of the "recommended" CPGs were warfarin, familial Mediterranean fever, and pediatric pulmonary arterial hypertension.The quality of CPGs for genetic testing in children was generally low, and variable across different CPGs and different AGREE II domains. In future guideline development, more attention should be paid to the aspects of stakeholder involvement, rigor of development, applicability, and editorial independence. Not only will guideline users benefit from our results when determining whether to adopt related CPGs to guide genetic testing in children, but guideline developers could also take into account our results to improve the quality of future CPGs.

A Retrospective Analysis of 10-Year Data Assessed the Diagnostic Accuracy and Efficacy of Cytogenomic Abnormalities in Current Prenatal and Pediatric Settings

Background: Array comparative genomic hybridization (aCGH), karyotyping and fluorescence in situ hybridization (FISH) analyses have been used in a clinical cytogenetic laboratory. A systematic analysis on diagnostic findings of cytogenomic abnormalities in current prenatal and pediatric settings provides approaches for future improvement.

Methods: A retrospective analysis was performed on abnormal findings by aCGH, karyotyping, and FISH from 3,608 prenatal cases and 4,509 pediatric cases during 2008–2017. The diagnostic accuracy was evaluated by comparing the abnormality detection rate (ADR) and the relative frequency (RF) of different types of cytogenomic abnormalities between prenatal and pediatric cases. A linear regression correlation between known prevalence and ADR of genomic disorders was used to extrapolate the prevalence of other genomic disorders. The diagnostic efficacy was estimated as percentage of detected abnormal cases by expected abnormal cases from served population.

Results: The composite ADR for numerical chromosome abnormalities, structural chromosome abnormalities, recurrent genomic disorders, and sporadic pathogenic copy number variants (pCNVs) in prenatal cases were 13.03%, 1.77%, 1.69%, and 0.9%, respectively, and were 5.13%, 2.84%, 7.08%, and 2.69% in pediatric cases, respectively. The chromosomal abnormalities detected in prenatal cases (14.80%) were significantly higher than that of pediatric cases (7.97%) (p < 0.05), while the pCNVs detected in prenatal cases (2.59%) were significantly lower than that of pediatric cases (9.77%) (p < 0.05). The prevalence of recurrent genomic disorders and total pCNVs was estimated to be 1/396 and 1/291, respectively. Approximately, 29% and 35% of cytogenomic abnormalities expected from the population served were detected in current prenatal and pediatric diagnostic practice, respectively.

Conclusion: For chromosomal abnormalities, effective detection of Down syndrome (DS) and Turner syndrome (TS) and under detection of sex chromosome numerical abnormalities in both prenatal and pediatric cases were noted. For pCNVs, under detection of pCNVs in prenatal cases and effective detection of DiGeorge syndrome (DGS) and variable efficacy in detecting other pCNVs in pediatric cases were noted. Extend aCGH analysis to more prenatal cases with fetal ultrasonographic anomalies, enhanced non-invasive prenatal (NIPT) testing screening for syndromic genomic disorders, and better clinical indications for pCNVs are approaches that could improve diagnostic yield of cytogenomic abnormalities.

Novel missense variant in TTN cosegregating with familial atrioventricular block

BACKGROUND

Cardiovascular diseases are the most common cause of death globally. In which atrioventricular block (AVB) is a common disorder with genetic causes, but the responsible genes have not been fully identified yet. To determine the underlying causative genes involved in cardiac AVB, here we report a three-generation Chinese family with severe autosomal dominant cardiac AVB that has been ruled out as being caused by known genes mutations.

METHODS

Whole-exome sequencing was performed in five affected family members across three generations, and co-segregation analysis was validated on other members of this family.

RESULTS

Whole-exome sequencing and subsequent co-segregation validation identified a novel germline heterozygous point missense mutation, c.49287C > A (p.N16429K), in the titin (TTN, NM_001267550.2) gene in all 5 affected family members but not in the unaffected family members, neither in the large population according to the Genome Aggregation Database (https://gnomad.broadinstitute.org/). The point mutation is predicted to be functionally deleterious by in-silico software tools. Our finding was further supported by the conservative analysis across species.

CONCLUSION

Based on this study, TTN was identified as a potential novel candidate gene for autosomal dominant AVB; this study expands the mutational spectrum of TTN gene and is the first to implicate TTN mutations as AVB disease causing in a Chinese pedigree.

Clinical use of SNP-microarrays for the detection of genome-wide changes in haematological malignancies

Single nucleotide polymorphism (SNP) microarrays are commonly used for the clinical investigation of constitutional genomic disorders; however, their adoption for investigating somatic changes is being recognised. With increasing importance being placed on defining the cancer genome, a shift in technology is imperative at a clinical level. Microarray platforms have the potential to become frontline testing, replacing or complementing standard investigations such as FISH or karyotype. This 'molecular karyotype approach' exemplified by SNP-microarrays has distinct advantages in the investigation of several haematological malignancies. A growing body of literature, including guidelines, has shown support for the use of SNP-microarrays in the clinical laboratory to aid in a more accurate definition of the cancer genome. Understanding the benefits of this technology along with discussing the barriers to its implementation is necessary for the development and incorporation of SNP-microarrays in a clinical laboratory for the investigation of haematological malignancies.

A novel case of global developmental delay syndrome with microdeletion at 10p14-p15.3 and microduplication at 18p11.31-p11.32

To characterize the etiology underlying a novel case of global developmental delay syndrome (GDDS) identified in a female child, aged 3 years old. This syndrome is a common pediatric presentation estimated to affect 3.65% of children aged 3 to 17 years.The proband's detailed family history was used to infer a likely mode of inheritance for the GDDS. Genomic DNA samples collected from the proband and her parents were evaluated using conventional karyotyping, multiplex ligation-dependent probe amplification (MLPA), comparative genomic hybridization microarray (aCGH), and fluorescent in situ hybridization (FISH) analysis techniques.An analysis of the proband's family history suggested that she inherited the GDDS from her father. The conducted conventional karyotyping and MLPA methods failed to identify a causative defect for the GDDS; however, the aCGH analysis revealed both a 6.6-Mb deletion at p14-p15.3 of chromosome 10 (arr[hg19]; 100,026-6,710,183), and a 6.3-Mb duplication at p11.31-p11.32 of chromosome 18 (arr[hg19]; 136,226-6,406,733) in the proband. The conducted FISH analysis subsequently determined that these mutations resulted from a balanced translocation t(10;18)(p15.3; p11.32) carried by the proband's father. Finally, a bioinformatic analysis of the proband's mutations revealed ZMYND11 as a promising candidate causative gene for this case of GDDS.The present study demonstrates that the aCGH method can be used to effectively identify the location and approximate size of microdeletions and/or microduplications, but not balanced reciprocal translocations. The nonconventional analysis methods used in the present study may be applicable to other GDDS cases with elusive etiology, and likewise, ZMYND11 should be considered as a potential causative gene during the investigation of future GDDS cases.

Experience of chromosomal microarray applied in prenatal and postnatal settings in Hong Kong

Chromosomal microarray (CMA) is recommended as a first tier investigation for patients with developmental delay (DD), intellectual disability (ID), autistic spectrum disorder (ASD), and multiple congenital anomalies (MCA). It is widely used in the prenatal and postnatal settings for detection of chromosomal aberrations. This is a retrospective review of all array comparative genomic hybridization (aCGH/ array CGH) findings ascertained in two major prenatal and postnatal genetic diagnostic centers in Hong Kong from June 2012 to December 2017. Medical records were reviewed for cases with pathogenic and variants of uncertain clinical significance (VUS). Classification of copy number variants (CNVs) was based on current knowledge and experience by August 2018. The aims of this review are to study the diagnostic yield of array CGH application in prenatal and postnatal settings in Hong Kong and to describe the spectrum of abnormalities found. Prenatal indications included abnormal ultrasound findings, positive Down syndrome screening, abnormal noninvasive prenatal test results, advanced maternal age and family history of chromosomal or genetic abnormalities. Postnatal indications included unexplained DD, ID, ASD, and MCA. A total of 1,261 prenatal subjects and 3,096 postnatal patients were reviewed. The prenatal diagnostic yield of pathogenic CNV and VUS (excluding those detectable by karyotype) was 3.5%. The postnatal diagnostic yield of pathogenic CNV was 15.2%. The detection rates for well-defined microdeletion and microduplication syndromes were 4.6% in prenatal and 6.1% (1 in 16 index patients) in postnatal cases, respectively. Chromosomes 15, 16, and 22 accounted for over 21 and 25% of pathogenic CNVs detected in prenatal and postnatal cohorts, respectively. This review provides the first large scale overview of genomic imbalance of mostly Chinese patients in prenatal and postnatal settings.

A Review of the Genomic Analysis of Children Presenting with Developmental Delay/Intellectual Disability and Associated Dysmorphic Features

This review describes the clinical criteria of developmental delay (DD)/intellectual disability (ID) as well as the various techniques that are currently implemented to diagnose neurodevelopmental disorders that typically present with associated dysmorphic features such as Angelman syndrome, Prader-Willi syndrome, and DiGeorge syndrome. These analyses include various forms of chromosomal microarray (CMA), which have proven to be superior to previously implemented techniques such as G-banded karyotyping and fluorescent in situ hybridization (FISH) analysis, as well as whole exome sequencing (WES), which is implemented as a secondary examination when CMA analysis is unrevealing. The clinical significance of identified variants and how it relates to facilitating the management of specific genetic disorders such as the above mentioned is also discussed. In addition, the importance of genomic databases and bioinformatics technologies as they relate to variant classification is also considered. Essentially, the discovery of pathogenic variants allows for enhanced management of a patient’s clinical phenotype, whereas the identification of variants of uncertain significance (VUS) has proven to have an increase in the number of associated conflicts as they typically generate more ambiguity in regard to the clinical manifestations present within the child. As a result, additional procedures need to be implemented to mitigate the issues that surround their identification. The concluding remarks are in regard to both the ethical and legal considerations of genetic testing as they relate to informed consent, testing of minors, how to handle secondary findings, as well as the anticipated future direction of genomic analysis.

Mutations in glucokinase and other genes detected in neonatal and type 1B diabetes patient using whole exome sequencing may lead to disease-causing changes in protein activity

Monogenic diabetes is caused by mutations that reduce β-cell function. While Sanger sequencing is the standard method used to detect mutated genes. Next-generation sequencing techniques, such as whole exome sequencing (WES), can be used to find multiple gene mutations in one assay. We used WES to detect genetic mutations in both permanent neonatal (PND) and type 1B diabetes (T1BD). A total of five PND and nine T1BD patients were enrolled in this study. WES variants were assessed using VarioWatch, excluding those identified previously. Sanger sequencing was used to confirm the mutations, and their pathogenicity was established via the literature or bioinformatic/functional analysis. The PND and T1BD patients were diagnosed at 0.1-0.5 and 0.8-2.7 years of age, respectively. Diabetic ketoacidosis was present at diagnosis in 60% of PND patients and 44.4% of T1BD patients. We found five novel mutations in five different genes. Notably, patient 602 had a novel homozygous missense mutation c.1295C > A (T432 K) in the glucokinase (GCK) gene. Compared to the wild-type recombinant protein, the mutant protein had significantly lower enzymatic activity (2.5%, p = 0.0002) and V_max (1.23 ± 0.019 vs. 0.33 ± 0.016, respectively; p = 0.005). WES is a robust technique that can be used to unravel the etiologies of genetically heterogeneous forms of diabetes. Homozygous inactivating mutations of the GCK gene may have a significant role in PND pathogenesis.

L’évaluation de l’enfant ayant un retard global du développement ou un handicap intellectuel

Le retard global du développement (RGD) et le handicap intellectuel (HI) font partie des problèmes courants en milieu pédiatrique. Leur étiologie est très hétérogène. L’American Academy of Pediatrics , l’American Academy of Neurology et le protocole Treatable Intellectual Disability Endeavor (TIDE) de la Colombie-Britannique préconisent des explorations du RGD et du HI en plusieurs étapes, afin d’orienter les médecins vers une recherche étiologique qui optimise le rendement thérapeutique. Le présent document de principes propose un cadre pour l’exploration clinique du RGD et du HI chez les enfants, de même qu’une mise à jour du protocole d’exploration étiologique que peuvent suivre les médecins canadiens. Le protocole révisé repose sur les connaissances à jour et les lignes directrices en place. Les principaux éléments de l’exploration comprennent des tests de la vision et de l’ouïe en bonne et due forme, l’analyse chromosomique sur micropuce, le test d’ADN du gène de l’X fragile et les tests de niveau 1 de dépistage des erreurs innées du métabolisme traitables. En cas de manifestations neurologiques particulières, l’imagerie cérébrale est recommandée.

Genetic Diagnostics for Neurologists

PURPOSE OF REVIEW

This article puts advances in the field of neurogenetics into context and provides a quick review of the broad concepts necessary for current practice in neurology.

RECENT FINDINGS

The exponential growth of genetic testing is due to its increased speed and decreasing cost, and it is now a routine part of the clinical care for a number of neurologic patients. In addition, phenotypic pleiotropy (mutations in the same gene causing very disparate phenotypes) and genetic heterogeneity (the same clinical phenotype resulting from mutations in different genes) are now known to exist in a number of conditions, adding an additional layer of complexity for genetic testing in these disorders.

SUMMARY

Although the growing complexity of technical knowledge in the ordering and interpretation of genetic tests makes it necessary for neurologists to consult medical geneticists, limitations in the availability of such professionals often means neurologists will be on the front line dealing with suspected or confirmed neurogenetic conditions. The growing availability of broad genetic testing through chromosomal microarray and next-generation sequencing and the expanded phenotypic spectrum of many conditions has implications for genetic counseling and medical management. This article discusses the various forms of genetic variability and how to test for each of them. It also provides an update on the most common forms of neurologic presentations of genetic disease and a review of testing strategies.

Evaluation of the child with global developmental delay and intellectual disability

Global developmental delay (GDD) and intellectual disability (ID) are common concerns in the paediatric setting. Etiologies of both conditions are highly heterogeneous. The American Academy of Pediatrics, the American Academy of Neurology and the British Columbia-based Treatable Intellectual Disability Endeavor (TIDE) protocol have each proposed multitiered investigations of GDD/ID to guide physicians toward an understanding of etiology that optimizes therapeutic yield. This statement provides a framework for the clinical investigation of GDD/ID in children, along with an updated protocol for Canadian physicians to follow in the etiological investigation of GDD/ID. The revised protocol is based on current knowledge and existing guidelines. Key elements of investigation include formal vision and hearing testing, chromosomal microarray, Fragile-X DNA testing and first-tier testing for treatable inborn errors of metabolism. Brain imaging is recommended in the presence of specific neurological findings.

An economic analysis of chromosome testing in couples with children who have structural chromosome abnormalities

Background

Structural chromosome abnormalities can cause significant negative reproductive outcomes as they typically result in morbidity and mortality of newborns. The prevalence of structural chromosomal abnormalities in live births is at least 0.05%, of which many of them have parental origins. It is uncommon to predict structural chromosome abnormalities at birth in the first child but it is possible to prevent repeated abnormalities through screening and diagnostic programmes. This study will provide an economic analysis of the prenatal detection of these abnormalities.

Methods

A cost-benefit analysis using a decision analytic model was employed to compare the status quo (doing nothing) with two interventional strategies. The first strategy (Strategy I) is preconceptional screening plus amniocentesis, and the second strategy (Strategy II) is amniocentesis alone. The monetary values in Thai baht (THB) were adjusted to international dollars (I$) using purchasing power parity (PPP) (I$1 = THB 17.60 for the year 2013). The robustness of the results was tested by applying a probabilistic sensitivity analysis.

Results

Both diagnostic strategies can reduce approximately 10.7–11.1 births with abnormal chromosomes per 1,000 diagnosed couples. The benefit cost ratios were 1.62 for Strategy I and 1.24 for Strategy II. Net present values per 1,000 diagnoses in couples were I$464,000 for Strategy I and I$267,000 for Strategy II. The probabilistic sensitivity analysis suggested that the cost-benefit analysis was sufficiently robust, confirming that both strategies provided higher benefits than costs.

Conclusions

Since the benefits of both diagnostic strategies exceeded their costs, both strategies are economical–with Strategy I being more economically attractive. Strategy I is superior to Strategy II because it decreases the risk of normal children potentially dying from the amniocentesis process.

Paediatricians underuse recommended genetic tests in children with global developmental delay

Objectives

To assess paediatricians' use of genetic testing for children with global developmental delay (GDD).

Study Design

We developed and piloted a questionnaire assessing the use of genetic tests in children with GDD and awareness of relevant guidelines. All practicing Quebec paediatricians were contacted. Paediatricians who did not evaluate children with GDD in their practice were excluded. Descriptive and statistical analyses were performed with SPSS.

Results

Of the 651 paediatricians, 225 answered (34.5%) and 141 were eligible. Only 31.9% were familiar with at least one guideline about genetic tests for the investigation of children with GDD, but 93.6% had ordered genetic testing for children with GDD (Fragile X testing [92.9%], karyotype [87.2%] and chromosomal microarray [63.8%]). Based on vignettes, 20.6% of participants would order genetic tests for isolated GDD and 95.0% for GDD with dysmorphic features and microcephaly. Only 56.7% ordered Fragile X testing for a girl with GDD and a known family history of Fragile X syndrome. Use of tests for isolated GDD was increased in presence of maternal pregnancy, compared with absence of pregnancy (44.7% and 27.7%, respectively). More participants would order genetic tests for a child with GDD and fetal exposure to alcohol (69.5%) than isolated GDD (20.6%).

Conclusions

Even though paediatricians often order genetic testing for children with GDD, practices and knowledge regarding testing are not optimal. As new and more complex genetic tests are developed, up-to-date training about the use of genetic tests for children with GDD needs to be integrated into paediatrics residency programs and continuous medical education.

A Novel 1.13 Mb Interstitial Duplication at 19q13.32 Causing Developmental Delay and Microcephaly in a Pediatric Patient: the First Asian Case Reports

Only 6 patients with partial trisomy of the long arm of chromosome 19 (19q), caused by direct interstitial duplications, have been reported until today. Herein, we report a pediatric patient with a novel 1.13 Mb direct interstitial duplication within 19q13.32, which is the smallest fragment affected so far. A five-year old Korean boy of healthy parents presented with microcephaly, growth retardation, developmental delay, and craniofacial dysmorphism. Even though G-banded chromosome analysis at resolution of 550-band revealed normal karyotype, duplication of 1.13 Mb fragment within 19q13.32 was detected by array comparative genomic hybridization. Comparing with previously reported patients with pure duplication involving 19q as a sole chromosomal abnormality, our case showed the smallest duplication segment with relatively mild degree of clinical features. Our present case might serve as the landmark case among patients with 19q duplication for genotype-phenotype correlation study and further identification of critical region for 19q duplication abnormalities.

Prenatal and Postnatal Genetic Testing: Why, How, and When?

There have been major advances in genetic testing especially over the last 10 years. We have advanced from looking at simple chromosomes under a microscope to more sophisticated analysis of the DNA makeup of chromosomes and from testing a single gene to sequencing almost all of our genetic material. Similarly, in the field of prenatal testing we have made great strides in screening and diagnostic testing in the hope of detecting significant abnormalities in the fetus while decreasing the risk to the pregnancy. In this article the major types of genetic screening and diagnostic testing, both prenatal and postnatal, will be reviewed. [Pediatr Ann. 2017;46(11):e423-e427.].

Potential Role of Genomic Sequencing in the Early Diagnosis of Treatable Genetic Conditions

We present cases of 3 children diagnosed with the same genetic condition, Gitelman syndrome, at different stages using various genetic methods: panel testing, targeted single gene sequencing, and exome sequencing. We discuss the advantages and disadvantages of each method and review the potential of genomic sequencing for early disease detection.

Utilization of genetic testing among children with developmental disabilities in the United States

Purpose

Several professional societies recommend that genetic testing be routinely included in the etiologic workup of children with developmental disabilities. The aim of this study was to determine the rate at which genetic testing is performed in this population, based on data from a nationally representative survey.

Methods

Data were analyzed from the Survey of Pathways to Diagnosis and Services, a telephone-based survey of parents and guardians of US school-age children with current or past developmental conditions. This study included 3,371 respondents who indicated that their child had an autism spectrum disorder (ASD), intellectual disability (ID), and/or developmental delay (DD) at the time of survey administration. History of genetic testing was assessed based on report by the parent/s. Children were divided into the following five mutually exclusive condition groups: ASD with ID; ASD with DD, without ID; ASD only, without ID or DD; ID without ASD; and DD only, without ID or ASD. Logistic regression was used to assess the demographic correlates of genetic testing, to compare the rates of genetic testing across groups, and to examine associations between genetic testing and use of other health-care services.

Results

Overall, 32% of this sample had a history of genetic testing, including 34% of all children with ASD and 43% of those with ID. After adjusting for demographics, children with ASD + ID were more than seven times as likely as those with ASD only, and more than twice as likely as those who had ID without ASD, to have undergone genetic testing. Prior specialist care (developmental pediatrician or neurologist) and access to all needed providers within the previous year were associated with higher odds of genetic testing.

Conclusion

The majority of children in this nationally representative sample did not undergo recommended genetic testing. Research is needed to identify barriers to the use of genetic testing in this population.

A novel CRX mutation by whole-exome sequencing in an autosomal dominant cone-rod dystrophy pedigree

AIM

To identify the disease-causing gene mutation in a Chinese pedigree with autosomal dominant cone-rod dystrophy (adCORD).

METHODS

A southern Chinese adCORD pedigree including 9 affected individuals was studied. Whole-exome sequencing (WES), coupling the Agilent whole-exome capture system to the Illumina HiSeq 2000 DNA sequencing platform was used to search the specific gene mutation in 3 affected family members and 1 unaffected member. After a suggested variant was found through the data analysis, the putative mutation was validated by Sanger DNA sequencing of samples from all available family members.

RESULTS

The results of both WES and Sanger sequencing revealed a novel nonsense mutation c.C766T (p.Q256X) within exon 5 of CRX gene which was pathogenic for adCORD in this family. The mutation could affect photoreceptor-specific gene expression with a dominant-negative effect and resulted in loss of the OTX tail, thus the mutant protein occupies the CRX-binding site in target promoters without establishing an interaction and, consequently, may block transactivation.

CONCLUSION

All modes of Mendelian inheritance in CORD have been observed, and genetic heterogeneity is a hallmark of CORD. Therefore, conventional genetic diagnosis of CORD would be time-consuming and labor-intensive. Our study indicated the robustness and cost-effectiveness of WES in the genetic diagnosis of CORD.

Clinical Impact and Cost-Effectiveness of Whole Exome Sequencing as a Diagnostic Tool: A Pediatric Center's Experience

BACKGROUND

There are limited reports of the use of whole exome sequencing (WES) as a clinical diagnostic tool. Moreover, there are no reports addressing the cost burden associated with genetic tests performed prior to WES.

OBJECTIVE

We demonstrate the performance characteristics of WES in a pediatric setting by describing our patient cohort, calculating the diagnostic yield, and detailing the patients for whom clinical management was altered. Moreover, we examined the potential cost-effectiveness of WES by examining the cost burden of diagnostic workups.

METHODS

To determine the clinical utility of our hospital's clinical WES, we performed a retrospective review of the first 40 cases. We utilized dual bioinformatics analyses pipelines based on commercially available software and in-house tools.

RESULTS

Of the first 40 clinical cases, we identified genetic defects in 12 (30%) patients, of which 47% of the mutations were previously unreported in the literature. Among the 12 patients with positive findings, seven have autosomal dominant disease and five have autosomal recessive disease. Ninety percent of the cohort opted to receive secondary findings and of those, secondary medical actionable results were returned in three cases. Among these positive cases, there are a number of novel mutations that are being reported here. The diagnostic workup included a significant number of genetic tests with microarray and single-gene sequencing being the most popular tests. Significantly, genetic diagnosis from WES led to altered patient medical management in positive cases.

CONCLUSION

We demonstrate the clinical utility of WES by establishing the clinical diagnostic rate and its impact on medical management in a large pediatric center. The cost-effectiveness of WES was demonstrated by ending the diagnostic odyssey in positive cases. Also, in some cases it may be most cost-effective to directly perform WES. WES provides a unique glimpse into the complexity of genetic disorders.

Paroxysmal kinesigenic dyskinesia caused by 16p11.2 microdeletion

BACKGROUND

Four cases of paroxysmal kinesigenic dyskinesia (PKD) have been reported in individuals with proximal 16p11.2 microdeletions that include PRRT2.

CASE REPORT

We describe a fifth patient with PKD, features of Asperger's syndrome, and mild language delays. Sanger sequencing of the PRRT2 gene did not identify any mutations implicated in PKD. However, microarray-based comparative genomic hybridization (aCGH) detected a 533.9-kb deletion on chromosome 16, encompassing over 20 genes and transcripts.

DISCUSSION

This case underscores the importance of aCGH testing for individuals with PKD who do not have PRRT2 mutations, particularly when developmental delays, speech problems, intellectual disability, and/or autism spectrum disorder are present.

Molecular findings among patients referred for clinical whole-exome sequencing

IMPORTANCE

Clinical whole-exome sequencing is increasingly used for diagnostic evaluation of patients with suspected genetic disorders.

OBJECTIVE

To perform clinical whole-exome sequencing and report (1) the rate of molecular diagnosis among phenotypic groups, (2) the spectrum of genetic alterations contributing to disease, and (3) the prevalence of medically actionable incidental findings such as FBN1 mutations causing Marfan syndrome.

DESIGN, SETTING, AND PATIENTS

Observational study of 2000 consecutive patients with clinical whole-exome sequencing analyzed between June 2012 and August 2014. Whole-exome sequencing tests were performed at a clinical genetics laboratory in the United States. Results were reported by clinical molecular geneticists certified by the American Board of Medical Genetics and Genomics. Tests were ordered by the patient's physician. The patients were primarily pediatric (1756 [88%]; mean age, 6 years; 888 females [44%], 1101 males [55%], and 11 fetuses [1% gender unknown]), demonstrating diverse clinical manifestations most often including nervous system dysfunction such as developmental delay.

MAIN OUTCOMES AND MEASURES

Whole-exome sequencing diagnosis rate overall and by phenotypic category, mode of inheritance, spectrum of genetic events, and reporting of incidental findings.

RESULTS

A molecular diagnosis was reported for 504 patients (25.2%) with 58% of the diagnostic mutations not previously reported. Molecular diagnosis rates for each phenotypic category were 143/526 (27.2%; 95% CI, 23.5%-31.2%) for the neurological group, 282/1147 (24.6%; 95% CI, 22.1%-27.2%) for the neurological plus other organ systems group, 30/83 (36.1%; 95% CI, 26.1%-47.5%) for the specific neurological group, and 49/244 (20.1%; 95% CI, 15.6%-25.8%) for the nonneurological group. The Mendelian disease patterns of the 527 molecular diagnoses included 280 (53.1%) autosomal dominant, 181 (34.3%) autosomal recessive (including 5 with uniparental disomy), 65 (12.3%) X-linked, and 1 (0.2%) mitochondrial. Of 504 patients with a molecular diagnosis, 23 (4.6%) had blended phenotypes resulting from 2 single gene defects. About 30% of the positive cases harbored mutations in disease genes reported since 2011. There were 95 medically actionable incidental findings in genes unrelated to the phenotype but with immediate implications for management in 92 patients (4.6%), including 59 patients (3%) with mutations in genes recommended for reporting by the American College of Medical Genetics and Genomics.

CONCLUSIONS AND RELEVANCE

Whole-exome sequencing provided a potential molecular diagnosis for 25% of a large cohort of patients referred for evaluation of suspected genetic conditions, including detection of rare genetic events and new mutations contributing to disease. The yield of whole-exome sequencing may offer advantages over traditional molecular diagnostic approaches in certain patients.

A refined approach to evaluating global developmental delay for the international medical community

BACKGROUND

Global developmental delay is usually defined as significant delay in two or more domains of development. Etiologic diagnosis generally proves difficult and the etiology remains undetermined in up to 62% of these children. Those in whom an etiology is established generally undergo an exhaustive and costly diagnostic evaluation, even though this may not change the medical or therapeutic management of the delay. The history and physical examination may provide up to 40% of etiologic diagnoses if adequately conducted.

METHODS

We performed a critical review of the literature on global developmental delay via PubMed.

RESULTS

Five major etiologic categories for global developmental delay were identified and traits of the history and physical examination suggestive for their diagnosis were described. Additionally, current diagnostic tools and their benefits and limitations were appraised.

CONCLUSIONS

We propose an improved approach to enhance clinical diagnosis in both resource-rich and resource-limited settings favoring early intervention and management.

The Developmental Brain Disorders Database (DBDB): a curated neurogenetics knowledge base with clinical and research applications

The number of single genes associated with neurodevelopmental disorders has increased dramatically over the past decade. The identification of causative genes for these disorders is important to clinical outcome as it allows for accurate assessment of prognosis, genetic counseling, delineation of natural history, inclusion in clinical trials, and in some cases determines therapy. Clinicians face the challenge of correctly identifying neurodevelopmental phenotypes, recognizing syndromes, and prioritizing the best candidate genes for testing. However, there is no central repository of definitions for many phenotypes, leading to errors of diagnosis. Additionally, there is no system of levels of evidence linking genes to phenotypes, making it difficult for clinicians to know which genes are most strongly associated with a given condition. We have developed the Developmental Brain Disorders Database (DBDB: https://www.dbdb.urmc.rochester.edu/home), a publicly available, online-curated repository of genes, phenotypes, and syndromes associated with neurodevelopmental disorders. DBDB contains the first referenced ontology of developmental brain phenotypes, and uses a novel system of levels of evidence for gene-phenotype associations. It is intended to assist clinicians in arriving at the correct diagnosis, select the most appropriate genetic test for that phenotype, and improve the care of patients with developmental brain disorders. For researchers interested in the discovery of novel genes for developmental brain disorders, DBDB provides a well-curated source of important genes against which research sequencing results can be compared. Finally, DBDB allows novel observations about the landscape of the neurogenetics knowledge base.

Identification of Chromosome Abnormalities in Subtelomeric Regions Using Multiplex Ligation Dependent Probe Amplification (MLPA) Technique in 100 Iranian Patients With Idiopathic Mental Retardation

Background

Mental retardation/Developmental delay (MR/DD) is present in 1 - 3% of the general population (1, 2). MR is defined as a significant impairment of both cognitive (IQ < 70) and social adaptive functions, with onset before 18 years of age.

Objectives

The purpose was to determine the results of subtelomeric screening by the Multiplex Ligation Dependent Probe Amplification (MLPA) Technique in 100 selected patients with idiopathic mental retardation (IMR) in Iran.

Materials and Methods

A number of 100 patients with IMR, normal karyotypes and negative fragile-X and metabolic tests were screened for subtelomeric abnormalities using MLPA technique.

Results

Nine of 100 patients showed subtelomeric abnormalities with at least one of the two MLPA kits. Deletion in a single region was found in 3 patients, and in two different subtelomeric regions in 1 patient. Duplication was only single and was present in 2 patients. Three patients were found to have both a deletion and duplication.MLPA testing in the parental samples of 7 patients which was accessible showed that 4 patients were de novo, 2 patients had inherited from a clinically normal mother, and one had inherited from a clinically normal father. Screening with the two MLPA kits (SALSA P036 and SALSA P070) proved abnormality in only five of the 9 patients.

Conclusions

So, the prevalence rate of abnormal subtelomeres using MLPA technique in patients with idiopathic MR in our study was 5 - 9%, the higher limit referring to the positive results of one of the two MLPA kits, and the lower limit representing the results of positive double-checking with the two MLPA kits.

Detection of chromosomal breakpoints in patients with developmental delay and speech disorders

Delineating candidate genes at the chromosomal breakpoint regions in the apparently balanced chromosome rearrangements (ABCR) has been shown to be more effective with the emergence of next-generation sequencing (NGS) technologies. We employed a large-insert (7-11 kb) paired-end tag sequencing technology (DNA-PET) to systematically analyze genome of four patients harbouring cytogenetically defined ABCR with neurodevelopmental symptoms, including developmental delay (DD) and speech disorders. We characterized structural variants (SVs) specific to each individual, including those matching the chromosomal breakpoints. Refinement of these regions by Sanger sequencing resulted in the identification of five disrupted genes in three individuals: guanine nucleotide binding protein, q polypeptide (GNAQ), RNA-binding protein, fox-1 homolog (RBFOX3), unc-5 homolog D (C.elegans) (UNC5D), transmembrane protein 47 (TMEM47), and X-linked inhibitor of apoptosis (XIAP). Among them, XIAP is the causative gene for the immunodeficiency phenotype seen in the patient. The remaining genes displayed specific expression in the fetal brain and have known biologically relevant functions in brain development, suggesting putative candidate genes for neurodevelopmental phenotypes. This study demonstrates the application of NGS technologies in mapping individual gene disruptions in ABCR as a resource for deciphering candidate genes in human neurodevelopmental disorders (NDDs).

Cytogenomic mapping and bioinformatic mining reveal interacting brain expressed genes for intellectual disability

BACKGROUND

Microarray analysis has been used as the first-tier genetic testing to detect chromosomal imbalances and copy number variants (CNVs) for pediatric patients with intellectual and developmental disabilities (ID/DD). To further investigate the candidate genes and underlying dosage-sensitive mechanisms related to ID, cytogenomic mapping of critical regions and bioinformatic mining of candidate brain-expressed genes (BEGs) and their functional interactions were performed. Critical regions of chromosomal imbalances and pathogenic CNVs were mapped by subtracting known benign CNVs from the Databases of Genomic Variants (DGV) and extracting smallest overlap regions with cases from DatabasE of Chromosomal Imbalance and Phenotype in Humans using Ensembl Resources (DECIPHER). BEGs from these critical regions were revealed by functional annotation using Database for Annotation, Visualization, and Integrated Discovery (DAVID) and by tissue expression pattern from Uniprot. Cross-region interrelations and functional networks of the BEGs were analyzed using Gene Relationships Across Implicated Loci (GRAIL) and Ingenuity Pathway Analysis (IPA).

RESULTS

Of the 1,354 patients analyzed by oligonucleotide array comparative genomic hybridization (aCGH), pathogenic abnormalities were detected in 176 patients including genomic disorders in 66 patients (37.5%), subtelomeric rearrangements in 45 patients (25.6%), interstitial imbalances in 33 patients (18.8%), chromosomal structural rearrangements in 17 patients (9.7%) and aneuploidies in 15 patients (8.5%). Subtractive and extractive mapping defined 82 disjointed critical regions from the detected abnormalities. A total of 461 BEGs was generated from 73 disjointed critical regions. Enrichment of central nervous system specific genes in these regions was noted. The number of BEGs increased with the size of the regions. A list of 108 candidate BEGs with significant cross region interrelation was identified by GRAIL and five significant gene networks involving cell cycle, cell-to-cell signaling, cellular assembly, cell morphology, and gene expression regulations were denoted by IPA.

CONCLUSIONS

These results characterized ID related cross-region interrelations and multiple networks of candidate BEGs from the detected genomic imbalances. Further experimental study of these BEGs and their interactions will lead to a better understanding of dosage-sensitive mechanisms and modifying effects of human mental development.

Clinical whole-exome sequencing for the diagnosis of mendelian disorders

BACKGROUND

Whole-exome sequencing is a diagnostic approach for the identification of molecular defects in patients with suspected genetic disorders.

METHODS

We developed technical, bioinformatic, interpretive, and validation pipelines for whole-exome sequencing in a certified clinical laboratory to identify sequence variants underlying disease phenotypes in patients.

RESULTS

We present data on the first 250 probands for whom referring physicians ordered whole-exome sequencing. Patients presented with a range of phenotypes suggesting potential genetic causes. Approximately 80% were children with neurologic phenotypes. Insurance coverage was similar to that for established genetic tests. We identified 86 mutated alleles that were highly likely to be causative in 62 of the 250 patients, achieving a 25% molecular diagnostic rate (95% confidence interval, 20 to 31). Among the 62 patients, 33 had autosomal dominant disease, 16 had autosomal recessive disease, and 9 had X-linked disease. A total of 4 probands received two nonoverlapping molecular diagnoses, which potentially challenged the clinical diagnosis that had been made on the basis of history and physical examination. A total of 83% of the autosomal dominant mutant alleles and 40% of the X-linked mutant alleles occurred de novo. Recurrent clinical phenotypes occurred in patients with mutations that were highly likely to be causative in the same genes and in different genes responsible for genetically heterogeneous disorders.

CONCLUSIONS

Whole-exome sequencing identified the underlying genetic defect in 25% of consecutive patients referred for evaluation of a possible genetic condition. (Funded by the National Human Genome Research Institute.).