186 research outputs found
Investigation of 90 patients referred for molecular cytogenetic analysis using aCGH uncovers previously unsuspected anomalies of imprinting
No full textThis study was an investigation of 90 patients referred to the Wessex Regional Genetics Laboratory for and negative by molecular cytogenetic analysis using array comparative genomic hybridization. This patient cohort represents typical referrals to a regional genetic centre. Methylation analysis was performed at 13 imprinted loci [PLAGL1, IGF2R, MEST, GRB10, H19, IGF2 DMR2 (IGF2P0), KCNQ1OT1 (KvDMR), MEG3, SNRPN, PEG3, GNAS (GNAS exon 1a and NESP55) and GNASAS]. In total 6/90 (6.67%) were shown to have a methylation defect, 2 of which were associated with known imprinting disorders: 1 patient had isolated hypomethylation at IGF2P0, an atypical epigenotype associated with Russell-Silver syndrome, and 1 showed hypomethylation at KvDMR consistent with a diagnosis of Beckwith-Wiedemann syndrome. A further 4 patients, 3 exhibiting complete hypermethylation, and 1 partial hypomethylation, had aberrations at IGF2R, the clinical significance of which remains unclear. This study demonstrates the potential utility of epigenetic investigation in routine diagnostic testing. <br/
Propionic Acidemia diagnosed in Amish adults and pregnancy outcomes: A case series
No full textBackground: Propionic acidemia (PA) is an inborn error of metabolism (IEM) that typically presents in the newborn. The Amish of North America have an increased prevalence of PA due to a founder variant in the PCCB gene. The Amish PA phenotype is variable, and some individuals remain asymptomatic and undiagnosed until adulthood. Additionally, there are limited reports of pregnancy outcomes in Amish individuals with PA. Methods: A retrospective single center chart review was completed on sixty Amish individuals with PA to identify individuals diagnosed as adults (18 years or older) and pregnancy outcomes. We assessed age at diagnosis, reason for PA testing, medical history prior to diagnosis including developmental delay, seizure, protein intolerance, cardiac symptoms, and anxiety. Following the diagnosis, we assessed the prevalence of prolonged QTc and dilated cardiomyopathy. We assessed our cohort for number of pregnancies, pregnancy outcomes, and peripartum complications. Results: Nine out of sixty individuals (15 %) were diagnosed with PA as adults. A family member with PA was the most common reason to prompt genetic testing. Cardiac symptoms were present in six of nine individuals prior to diagnosis. Three individuals diagnosed as adults had dilated cardiomyopathy and one underwent cardiac transplant. There were twenty-one pregnancies in six women with eighteen successful deliveries and three miscarriages. Two women developed peripartum cardiomyopathy. There were no acute maternal decompensations. Conclusion: Our work supports the consideration that all Amish newborns be screened for PA with molecular testing to enable early diagnosis. The stark difference in peripartum outcomes requires further prospective work to ensure appropriate monitoring throughout pregnancy while respecting individual values and autonomy
Expanding the genetic spectrum of hereditary motor sensory neuropathies in Pakistan
No full textBACKGROUND: Hereditary motor and sensory neuropathy (HMSN) refers to a group of inherited progressive peripheral neuropathies characterized by reduced nerve conduction velocity with chronic segmental demyelination and/or axonal degeneration. HMSN is highly clinically and genetically heterogeneous with multiple inheritance patterns and phenotypic overlap with other inherited neuropathies and neurodegenerative diseases. Due to this high complexity and genetic heterogeneity, this study aimed to elucidate the genetic causes of HMSN in Pakistani families using Whole Exome Sequencing (WES) for variant identification and Sanger sequencing for validation and segregation analysis, facilitating accurate clinical diagnosis. METHODS: Families from Khyber Pakhtunkhwa with at least two members showing HMSN symptoms, who had not previously undergone genetic analysis, were included. Referrals for genetic investigations were based on clinical features suggestive of HMSN by local neurologists. WES was performed on affected individuals from each family, with Sanger sequencing used to validate and analyze the segregation of identified variants among family members. Clinical data including age of onset were assessed for variability among affected individuals, and the success rate of genetic diagnosis was compared with existing literature using proportional differences and Cohen's h. RESULTS: WES identified homozygous pathogenic variants in GDAP1 (c.310 + 4 A > G, p.?), SETX (c.5948_5949del, p.(Asn1984Profs*30), IGHMBP2 (c.1591 C > A, p.(Pro531Thr) and NARS1 (c.1633 C > T, p.(Arg545Cys) as causative for HMSN in five out of nine families, consistent with an autosomal recessive inheritance pattern. Additionally, in families with HMSN, a SETX variant was found to cause cerebellar ataxia, while a NARS1 variant was linked to intellectual disability. Based on American College of Medical Genetics and Genomics criteria, the GDAP1 variant is classified as a variant of uncertain significance, while variants in SETX and IGHMBP2 are classified as pathogenic, and the NARS1 variant is classified as likely pathogenic. The age of onset ranged from 1 to 15 years (Mean = 5.13, SD = 3.61), and a genetic diagnosis was achieved in 55.56% of families with HMSN, with small effect sizes compared to previous studies. CONCLUSIONS: This study expands the molecular genetic spectrum of HMSN and HMSN plus type neuropathies in Pakistan and facilitates accurate diagnosis, genetic counseling, and clinical management for affected families.Journal content freely available via Open Access. Some content may be unavailable due to publisher embargo. Click on the 'Additional link' above to access the full-text
PRUNE1: a disease-causing gene for secondary microcephaly
No full textIn their Letter to the Editor, Karakaya et al. (2017) present
an interesting case report describing the clinical course
involving secondary microcephaly of a 3-year-old Turkish
boy found to be homozygous for a frameshift mutation in
PRUNE1 identified through whole exome sequencing. The
child presented with congenital hypotonia, contractures and
global developmental delay with respiratory insufficiency
and seizures developing in the first year of life. The authors
note that the affected child’s head circumference plotted on
the 75th centile at birth, and that by 38 months of age he
had developed microcephaly. Neuroimaging at 14 months
revealed cerebral and cerebellar atrophy consistent with
other patients described with Prune syndrome (Karaca
et al., 2015; Costain et al., 2017; Zollo et al., 2017).
Although the child had abnormal neurology from birth,
there was a period of early developmental regression.
Peripheral spasticity in the lower extremities and optic atrophy
were not documented until 38 months. In addition to
the PRUNE1 variant, Karakaya et al. also identified a
second homozygous variant in the CCDC14 gene in the
Turkish child’s whole exome sequencing data that, while
listed to have an allele count of 108 in the current Genome
Aggregation Database (gnomAD) release, is notably absent
in homozygous fashion (Lek et al., 2016). CCDC14 is
known to be expressed in human brain, reported to negatively
regulate centriole duplication and interact with proteins
previously associated with primary microcephaly
(Firat-Karalar et al., 2014). Thus, while it seems likely
that the homozygous PRUNE1 variant is primarily responsible
for the clinical presentation in the Turkish child, it is
impossible to determine whether there may be any phenotypical
contribution from this additional homozygous
sequence variant.
Recently, Costain et al. (2017) described a homozygous
consensus splice site variant in PRUNE1 (c.521-2A4G;
NM_021222.1) in a 2-year-old Oji-Cre male who presented
with congenital hypotonia and talipes, whose head circumference
was large at birth ( +3 standard deviations), but by
2 years and 2 months plotted on the 50th centile, with a
weight and height on the 95th and 75th centiles, respectively.
However, it should be noted that the child’s father
is macrocephalic ( +4 standard deviations), the published
clinical photographs at 2 years 5 months of age illustrate
bitemporal narrowing, a sloping forehead and large ears,
consistent with a developing microcephaly, and neuroimaging revealed cortical and cerebellar atrophy. He
developed respiratory insufficiency shortly after birth, and
infantile spasms in the first year of life (Costain et al., 2017).
It remains to be determined how the phenotypical outcomes
stemming from proposed loss-of-function mutations
defined by Karakaya et al. and Costain et al., relate to
missense mutations published by Karaca et al. and also
Zollo et al., which are likely to involve at least partial
gain-of-function outcomes in PRUNE1 activity. However,
as more cases are investigated and published, the phenotype
associated with autosomal recessive Prune neurodevelopmental
disorder, and the functional outcomes of
PRUNE1 mutation, are becoming clearer. It is now apparent
that while some patients have a small head at birth and
others a head circumference in the normal range, the key
component of the microcephaly is that it is progressive, and
associated with characteristic neuroimaging findings with a
thin or hypoplastic corpus callosum and cortical and cerebellar
atrophy developing in early childhood. Although all
patients with Prune syndrome described to date are neurologically
impaired from birth, there also appears to be a
neurodegenerative component with progression of the disorder.
In our manuscript, we described clinical overlap of
Prune syndrome with the neurodegenerative condition associated
with homozygous mutations in TBCD (Zollo et al.,
2017). TBCD encodes one of the five tubulin-specific chaperones
that are required for a/b-tubulin de novo heterodimer
formation and the disorder is characterized by
developmental regression, seizures, optic atrophy and secondary
microcephaly, cortical atrophy with delayed myelination,
cerebellar atrophy and thinned corpus callosum
(Edvardson et al., 2016; Flex et al., 2016; Miyake et al.,
2016; Pode-Shakked et al., 2017). The neurodegenerative
phenotype documented in the Turkish child by Karakaya
et al. further demonstrates the similarities with the TBCD
disorder and Prune syndrome, and confirms optic atrophy
to be a feature of Prune syndrome. Interestingly, it is also
becoming clear that respiratory insufficiency is a common
feature of Prune syndrome, having been documented by
Karakaya et al. and in the Oji-Cre child, as well as the
youngest affected Omani child described in our manuscript
Investigation of the Molecular Basis of Primary Ciliary Dyskinesia and Situs Inversus amongst the Amish
No full textCilia are hair-like projections from eukaryotic cells: they are complex organelles that can be split into motile (normal/embryonic nodal) and non-motile types. Primary ciliary dyskinesia (PCD) is genetically heterogeneous, typically autosomal recessive disorder, characterised by oto-sino-pulmonary disease, male infertility and situs abnormalities, due to structural and motion defects of cilia. Early diagnosis and specialist intervention significantly improves clinical outcome. Situs inversus (SI) is a related condition involving, the mirror image rearrangement of the internal organs and has a more complex genetic basis; it can also be a component of a more complex syndrome. Pathogenic variants in >40 genes have been associated with these conditions, accounting for <70% of cases.
This project is part of a long-running clinical-genetic program based amongst the Amish communities in the USA which aims to define the frequencies and genetic causes of PCD/SI. A combination of clinical phenotyping, autozygosity mapping, and whole exome sequencing, were used to investigate Amish families affected by these disorders. This enabled the identification of the novel disease genes in each case. This study determined that both PCD and SI occur more commonly amongst the Amish than in non-Amish families. Genomic studies of affected individuals identified known causes of PCD, as well as two putative novel causes of PCD/SI. Notably, previous studies of knockout mice for one of the new candidate genes identified SI as a key phenotype, overlapping with the human condition. Preliminary genetic studies in other families with PCD and situs abnormalities failed to identify clear genetic causes, so studies are ongoing to investigate more complex pathogenesis. While additional work is required to define the outcome of the sequence variants identified, these studies provide a greatly improved understanding of the frequencies and causes of PCD/SI in the Amish, and define two putative new candidate genetic causes
Investigating the genetic basis of hereditary spastic paraplegia and cerebellar Ataxia in Pakistani families
No full textBACKGROUND: Hereditary Spastic Paraplegias (HSPs) and Hereditary Cerebellar Ataxias (HCAs) are progressive neurodegenerative disorders encompassing a spectrum of neurogenetic conditions with significant overlaps of clinical features. Spastic ataxias are a group of conditions that have features of both cerebellar ataxia and spasticity, and these conditions are frequently clinically challenging to distinguish. Accurate genetic diagnosis is crucial but challenging, particularly in resource-limited settings. This study aims to investigate the genetic basis of HSPs and HCAs in Pakistani families. METHODS: Families from Khyber Pakhtunkhwa with at least two members showing HSP or HCA phenotypes, and who had not previously been analyzed genetically, were included. Families were referred for genetic analysis by local neurologists based on the proband's clinical features and signs of a potential genetic neurodegenerative disorder. Whole Exome Sequencing (WES) and Sanger sequencing were then used to identify and validate genetic variants, and to analyze variant segregation within families to determine inheritance patterns. The mean age of onset and standard deviation were calculated to assess variability among affected individuals, and the success rate was compared with literature reports using differences in proportions and Cohen's h. RESULTS: Pathogenic variants associated with these conditions were identified in five of eight families, segregating according to autosomal recessive inheritance. These variants included previously reported SACS c.2182 C > T, p.(Arg728*), FA2H c.159_176del, p.(Arg53_Ile58del) and SPG11 c.2146 C > T, p.(Gln716*) variants, and two previously unreported variants in SACS c.2229del, p.(Phe743Leufs*8) and ZFYVE26 c.1926_1941del, p.(Tyr643Metfs*2). Additionally, FA2H and SPG11 variants were found to have recurrent occurrences, suggesting a potential founder effect within the Pakistani population. Onset age among affected individuals ranged from 1 to 14 years (M = 6.23, SD = 3.96). The diagnostic success rate was 62.5%, with moderate effect sizes compared to previous studies. CONCLUSIONS: The findings of this study expand the genotypic and phenotypic spectrum of HSPs and HCAs in Pakistan and emphasize the importance of utilizing exome/genome sequencing for accurate diagnosis or support accurate differential diagnosis. This approach can improve genetic counseling and clinical management, addressing the challenges of diagnosing neurodegenerative disorders in resource-limited settings.This article is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License, which permits any non-commercial use, sharing, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if you modified the licensed material. You do not have permission under this licence to share adapted material derived from this article or parts of it. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by-nc-nd/4.0/Journal content freely available via Open Access. Some content may be unavailable due to publisher embargo. Click on the 'Additional link' above to access the full-text
Delineating the clinical, genetic and molecular characteristics of neurodevelopmental disorders in a community setting
No full textInherited neurodevelopmental disorders are a large group of clinically and genetically heterogeneous conditions affecting the development, structure and functioning of the central nervous system, and are frequently associated with extremes of brain growth. Whilst specific neurodevelopmental disorders are typically individually rare, as a group these conditions comprise a significant healthcare burden globally. A significant contribution to our understanding of neurodevelopmental disorders has been made by the study of autosomal recessive conditions, which are rare in the general population but occur at increased frequency in certain genetically isolated communities due to founder gene variants. The studies described in this thesis entail clinical, genetic and functional studies of inherited single gene disorders of brain growth identified in North American Amish and rural Pakistani communities, leading to investigations in other families globally.
Chapter three describes the identification of a microcephalic neurodevelopmental disorder resulting from biallelic variants in the TRAPPC10 gene, encoding a transport protein particle (TRAPP) complex subunit involved in membrane trafficking and other cellular processes. This study, stemming from genetic findings in two Pakistani families harbouring distinct TRAPPC10 variants, entailed comprehensive clinical, genomic, mouse and functional studies to confirm TRAPPC10-related disorder as a novel TRAPPopathy. This chapter also describes preliminary clinical and genetic studies identifying or consolidating five further TRAPPopathy disorders.
KPTN-related megalencephalic neurodevelopmental disorder was first identified by our research group in 2014. Chapter four documents the most detailed phenotypic description of the condition to date, alongside genetic findings of 36 affected individuals identified through international collaboration. This work enabled preliminary genotype-phenotype correlations to be drawn and patient management guidelines to be developed. Additionally, detailed comparisons with a Kptn-/- knock-out mouse model that closely recapitulates the human disease, alongside cell studies, provided fundamental new insights into the condition. Together, this enabled KPTN-related disorder to be confirmed as a new mTORopathy, highlighting the potential of mTOR inhibitors as a candidate therapeutic option for the condition.
Chapter five details extensive clinical and genetic datasets to consolidate and more comprehensively define two previously poorly described causes of autosomal recessive disorders of brain growth and development. These involve variants in CEP55 associated with a severe lethal fetal disorder characterised by a variable spectrum of brain and kidney abnormalities, and INPP4A associated with a variable neurodevelopmental disorder with features of severe cognitive impairment, seizures, muscle weakness, cerebellar signs, spasticity and behavioural abnormalities.
The clinical, genetic and molecular delineation of rare neurodevelopmental disorders facilitates accurate diagnosis and management of these conditions. The work described in this thesis also provides invaluable insights into disease pathogenesis and improves the scientific understanding of the subcellular processes underlying neurodevelopment. This knowledge is crucial to ultimately enable the discovery and delivery of potential new therapeutic avenues to treat these disorders
Targeted methylation testing of a patient cohort broadens the epigenetic and clinical description of imprinting disorders
No full textImprinting disorders are associated with mutations and epimutations affecting imprinted genes, that is those whose expression is restricted by parent of origin. Their diagnosis is challenging for two reasons: firstly, their clinical features, particularly prenatal and postnatal growth disturbance, are heterogeneous and partially overlapping; secondly, their underlying molecular defects include mutation, epimutation, copy number variation, and chromosomal errors, and can be further complicated by somatic mosaicism and multi-locus methylation defects. It is currently unclear to what extent the observed phenotypic heterogeneity reflects the underlying molecular pathophysiology; in particular, the molecular and clinical diversity of multilocus methylation defects remains uncertain. To address these issues we performed comprehensive methylation analysis of imprinted genes in a research cohort of 285 patients with clinical features of imprinting disorders, with or without a positive molecular diagnosis. 20 of 91 patients (22%) with diagnosed epimutations had methylation defects of additional imprinted loci, and the frequency of developmental delay and congenital anomalies was higher among these patients than those with isolated epimutations, indicating that hypomethylation of multiple imprinted loci is associated with increased diversity of clinical presentation. Among 194 patients with clinical features of an imprinting disorder but no molecular diagnosis, we found 15 (8%) with methylation anomalies, including missed and unexpected molecular diagnoses. These observations broaden the phenotypic and epigenetic definitions of imprinting disorders, and show the importance of comprehensive molecular testing for patient diagnosis and management
Mutational spectrum associated with oculocutaneous albinism and Hermansky-Pudlak syndrome in nine Pakistani families
No full textBACKGROUND: Oculocutaneous albinism (OCA) is a genetically heterogeneous condition that is associated with reduced or absent melanin pigment in the skin, hair, and eyes, resulting in reduced vision, high sensitivity to light, and rapid and uncontrolled eye movements. To date, seventeen genes have been associated with OCA including syndromic and non-syndromic forms of the condition. METHODS: Whole exome sequencing (WES) was performed to identify pathogenic variants in nine Pakistani families with OCA, with validation and segregation of candidate variants performed using Sanger sequencing. Furthermore, the pathogenicity of the identified variants was assessed using various in-silico tools and 3D protein structural analysis software. RESULTS: WES identified biallelic variants in three genes explaining the OCA in these families, including four variants in TYR, three in OCA2, and two in HPS1, including two novel variants c.667C > T: p.(Gln223*) in TYR, and c.2009 T > C: p.(Leu670Pro) in HPS1. CONCLUSIONS: Overall, this study adds further knowledge of the genetic basis of OCA in Pakistani communities and facilitates improved management and counselling services for families suffering from severe genetic diseases in Pakistan.Published version, accepted versionJournal content freely available via Open Access. Some content may be unavailable due to publisher embargo. Click on the 'Additional link' above to access the full-text
An atypical case of hypomethylation at multiple imprinted loci
No full textAngelman syndrome (AS) and Prader–Willi syndrome (PWS) are caused by genetic and epigenetic mutations of the imprinted gene cluster on chromosome 15q13. Although the imprinting mutations causing PWS and AS are essentially opposite in nature, remarkably, a small number of patients have been reported with clinical features of PWS but epigenetic mutations consistent with AS. We report here a patient who presented with clinical features partially consistent with both PWS and Beckwith–Wiedemann syndrome (BWS). Epimutations were found at both the AS/PWS and BWS loci, and additionally at the H19, PEG3, NESPAS and GNAS loci. This patient is therefore the first described case with a primary epimutation consistent with AS accompanied by hypomethylation of other imprinted loci.<br/
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