Clinical experience of next generation sequencing based expanded carrier screening in high-risk couples from a tertiary healthcare center in Pakistan.

INTRODUCTION: Carrier screening for genetic conditions has long been a part of preconception and prenatal care. While the use of expanded carrier screening (ECS) is widely common in HICs (high income countries), the clinical actionability of ECS in LMICs (low middle income countries) with high consanguineous unions is not well-understood. METHOD: Retrospective chart review of couples who presented to the Prenatal Genetics Clinic at Aga Khan University Hospital, between the period of June 2018 and November 2022. All the statistical analyses were performed using the statistical software STATA version 17.0. RESULTS: Of the 202 individuals tested, 166 (82%) were identified to be carriers of at least one gene associated with a monogenic condition. Out of the 302 genes tested, individuals were found to be carriers of conditions associated with 87 genes. Clinical actionability of ECS was established in a total of 45 (45%) high risk couples undergoing screening using ECS. CONCLUSION: We report the first clinical experience of using next generation sequencing based ECS in 101 high-risk couples seeking consultation in the Genetics Clinic, at a tertiary healthcare center in Pakistan, showing that over 80% high-risk individuals are carriers of at least one condition and 45% of couples receive an actionable result to making autonomous informed reproductive decisions in future pregnancies.

Evaluation of the clinical, biochemical, and molecular spectrum of Cobalamin C (CblC) defect in 33 patients from Pakistan.

BACKGROUND: Cobalamin C is the most common inborn error of intracellular cobalamin metabolism caused by biallelic pathogenic variants in the MMACHC gene, leading to impaired conversion of dietary vitamin B12 into its two metabolically active forms, methylcobalamin and adenosylcobalamin. Biochemical hallmarks are elevated plasma total homocysteine (HCYs) and low methionine accompanied by methylmalonic aciduria. This study aimed to evaluate the clinical, biochemical, and molecular analysis of Pakistani patients with CblC defect. METHODS: Medical charts, urine organic acid (UOA) chromatograms, plasma amino acid levels, plasma tHcy and MMACHC gene results of patients presenting at the Biochemical Genetics Clinic, AKUH from 2013-2021 were reviewed. Details were collected on a pre-structured questionnaire. SPSS 22 was used for data analysis. RESULTS: CblC was found in 33 cases (Male:Female 19:14). The median age of symptoms onset and diagnosis were 300 (IQR:135-1800) and 1380 (IQR: 240-2730) days. The most common clinical features were cognitive impairment (n = 29), seizures (n = 23), motor developmental delay (n = 20), hypotonia (n = 17), and sparse/hypopigmented scalp hair (n = 16). The MMACHC gene sequencing revealed homozygous pathogenic variant c.394C > T, (p.Arg132*) in 32 patients, whereas c.609G > A, (p.TRP203*) in one patient whose ancestors had settled in Pakistan from China decades ago. The median age of treatment initiation was 1530 (IQR: 240-2790). The median pre-treatment HCYs levels were 134 (IQR:87.2-155.5) compared to post-treatment levels of 33.3 (IQR: 27.3-44.95) umol/L. CONCLUSIONS: Thirty-three cases of CblC defect from a single center underscores a significant number of the disorder within Pakistan. Late diagnosis emphasizes the need for increased clinical awareness and adequate diagnostic facilities.

The spectrum of hereditary neuromuscular disorders in the Pakistani population.

Hereditary neuromuscular disorders (NMDs) are a broad group of clinically heterogeneous disorders with varying inheritance patterns, that are associated with over 500 implicated genes. In the context of a highly consanguineous Pakistani population, we expect that autosomal recessive NMDs may have a higher prevalence compared with patients of European descent. This is the first study to offer a detailed description of the spectrum of genes causing hereditary NMDs in the Pakistani population using NGS testing. To study the clinical and genetic profiles of patients presenting for evaluation of a hereditary neuromuscular disorder. This is a retrospective chart review of patients seen in the Neuromuscular Disorders Clinic and referred to the Genetics Clinic with a suspected hereditary neuromuscular disorder, between 2016 and 2020 at the Aga Khan University Hospital, Karachi and Mukhtiar A. Sheikh Hospital, Multan, Pakistan. The genetic testing for these patients included NGS-based single gene sequencing, NGS-based multi-gene panel and whole exome sequencing. In a total of 112 patients studied, 35 (31.3%) were female. The mean age of onset in all patients was 14.6 years (SD ±12.1 years), with the average age at presentation to the clinic of 22.4 years (SD ±14.10 years). Forty-seven (41.9%) patients had a positive genetic test result, 53 (47.3%) had one or more variants of uncertain significance (VUS), and 12 (10.7%) had a negative result. Upon further genotype-phenotype correlation and family segregation analysis, the diagnostic yield improved, with 59 (52.7%) patients reaching a diagnosis of a hereditary NMD. We also report probable founder variants in COL6A2, FKTN, GNE, and SGCB, previously reported in populations that have possible shared ancestry with the Pakistani population. Our findings reemphasizes that the rate of VUSs can be reduced by clinical correlation and family segregation studies.

Experience in prenatal genetic testing and reproductive decision-making for monogenic disorders from a single tertiary care genetics clinic in a low-middle income country.

OBJECTIVES: Explore health-care seeking behaviour among couples with pregnancies at-risk of monogenic disorders and compare time duration for obtaining Prenatal Genetic Test (PGT) results based on (i) amniocentesis and Chorionic Villus Sampling (CVS) (ii) in-house testing and out-sourced testing. Report the spectrum of monogenic disorders in our cohort. METHODS: Medical records of women consulting prenatal genetic counselling clinic at Aga Khan University Hospital, Karachi from December-2015 to March-2021 with history of miscarriage or a monogenic disorder in previous children were reviewed. RESULTS: Forty-three pregnancies in 40 couples were evaluated, 37(93%) were consanguineous. Twenty-five (63%) couples consulted before and 15(37%) after conception. Thirty-one (71%) pregnancies underwent CVS at the mean gestational age of 13-weeks and 6-days ± 1-week and 3-days and amniocentesis at 16-weeks and 2-days ± 1-week and 4-days. PGT for 30 (70%) pregnancies was outsourced. The mean number of days for in-house PGT was 16.92 ± 7.80 days whereas for outsourced was 25.45 ± 7.7 days. Mean duration from procedure to PGT result was 20.55 days after CVS compared to 28.75 days after amniocentesis. Eight (18%) fetuses were homozygous for disease-causing variant for whom couples opted for termination of pregnancy (TOP). Twenty-six monogenetic disorders were identified in 40 families. CONCLUSION: Proactive health-care seeking behaviour and TOP acceptance is present amongst couples who have experienced a genetic disorder.

Blue rubber bleb nevus syndrome in a Pakistani child: A case report and regional literature review.

Blue rubber bleb nevus syndrome (BRBNS) is a rare disorder in which there is development of multiple venous malformations and haemangiomas in the skin and visceral organs. The lesions mostly involve the skin and gastrointestinal systems but other organs, including the liver, muscles, and the central nervous system, can also be involved. If untreated, affected individuals develop severe anaemia. Most cases are managed with iron supplementation and blood transfusions but some may require surgical resection, endoscopic sclerosis and laser photocoagulation. Here, we present a case of BRBNS in a four-year-old girl with multiple cutaneous lesions, melena and severe anaemia. Review of South Asian literature showed that only two cases (besides ours) have been reported from Pakistan and the rest were from India. This highlights the lack of awareness of BRBNS among physicians in Pakistan and the rest of South Asian countries.

A descriptive case series of necrotising enterocolitis; occurrence at Aga Khan University Hospital.

The objective of this study was to determine the frequency and outcome of preterm infants diagnosed with Necrotising Enterocolitis (NEC). In a case series, 320 preterm infants were enrolled during a period of 12 months at Aga Khan University Hospital, Karachi, a tertiary care hospital. Diagnosis and staging was done as per Bell's staging criteria. Possible confounders were filtered. Analysis was based on the form of treatment and symptom progression. During the study, NEC was observed in 29(9.06%) babies of which stages I, II and III were 69%, 24% and 7%, respectively. Outcome analysis showed that among the 29 neonates diagnosed with NEC, 23 were discharged and 6 expired. A 9% prevalence observed during the study suggests this to be to be a major challenge in neonatology. Mortality outcome of 21% diagnosed with NEC recommends an early diagnosis coupled with prompt and appropriate treatment and preventive measures to reduce the burden of NEC in future.

Perspective on newborn screening (NBS): Evidence sharing on conditions to be included in NBS in Pakistan.

Newborn screening aims at detecting treatable disorders early so that the treatment can be initiated to prevent mortality and morbidity. Such programmes are well established in most developed countries, and all newborns are screened for selected metabolic, endocrine and other disorders based on disease epidemiology, testing and treatment availability, efficiency and cost-effectiveness. Even in developing countries, such screening programmes are initiated using heel prick capillary blood collected on filter paper. The current narrative review was planned to provide a perspective with evidence in favour of starting newborn screening for different disorders. The programme project should be initiated nationwide, taking one disorder, congenital hypothyroidism, as the prototype and a newborn screening panel can then be extended to include other disorders. A task force should be set up to recommend disorders to be included in the panel, develop the national plan policies, and define procedures to strengthen the testing.

A pathogenic UFSP2 variant in an autosomal recessive form of pediatric neurodevelopmental anomalies and epilepsy.

PURPOSE: Neurodevelopmental disabilities are common and genetically heterogeneous. We identified a homozygous variant in the gene encoding UFM1-specific peptidase 2 (UFSP2), which participates in the UFMylation pathway of protein modification. UFSP2 variants are implicated in autosomal dominant skeletal dysplasias, but not neurodevelopmental disorders. Homozygosity for the variant occurred in eight children from four South Asian families with neurodevelopmental delay and epilepsy. We describe the clinical consequences of this variant and its effect on UFMylation. METHODS: Exome sequencing was used to detect potentially pathogenic variants and identify shared regions of homozygosity. Immunoblotting assessed protein expression and post-translational modifications in patient-derived fibroblasts. RESULTS: The variant (c.344T>A; p.V115E) is rare and alters a conserved residue in UFSP2. Immunoblotting in patient-derived fibroblasts revealed reduced UFSP2 abundance and increased abundance of UFMylated targets, indicating the variant may impair de-UFMylation rather than UFMylation. Reconstituting patient-derived fibroblasts with wild-type UFSP2 reduced UFMylation marks. Analysis of UFSP2's structure indicated that variants observed in skeletal disorders localize to the catalytic domain, whereas V115 resides in an N-terminal domain possibly involved in substrate binding. CONCLUSION: Different UFSP2 variants cause markedly different diseases, with homozygosity for V115E causing a severe syndrome of neurodevelopmental disability and epilepsy.

PIGG variant pathogenicity assessment reveals characteristic features within 19 families.

PURPOSE: Phosphatidylinositol Glycan Anchor Biosynthesis, class G (PIGG) is an ethanolamine phosphate transferase catalyzing the modification of glycosylphosphatidylinositol (GPI). GPI serves as an anchor on the cell membrane for surface proteins called GPI-anchored proteins (GPI-APs). Pathogenic variants in genes involved in the biosynthesis of GPI cause inherited GPI deficiency (IGD), which still needs to be further characterized. METHODS: We describe 22 individuals from 19 unrelated families with biallelic variants in PIGG. We analyzed GPI-AP surface levels on granulocytes and fibroblasts for three and two individuals, respectively. We demonstrated enzymatic activity defects for PIGG variants in vitro in a PIGG/PIGO double knockout system. RESULTS: Phenotypic analysis of reported individuals reveals shared PIGG deficiency-associated features. All tested GPI-APs were unchanged on granulocytes whereas CD73 level in fibroblasts was decreased. In addition to classic IGD symptoms such as hypotonia, intellectual disability/developmental delay (ID/DD), and seizures, individuals with PIGG variants of null or severely decreased activity showed cerebellar atrophy, various neurological manifestations, and mitochondrial dysfunction, a feature increasingly recognized in IGDs. Individuals with mildly decreased activity showed autism spectrum disorder. CONCLUSION: This in vitro system is a useful method to validate the pathogenicity of variants in PIGG and to study PIGG physiological functions.

Clinico-Pathological and Molecular Spectrum of Biotinidase Deficiency- Experience from a Lower Middle-Income Country.

BACKGROUND: The aim of this study was to evaluate the clinical, biochemical, and molecular analysis of Pakistani patients with biotinidase deficiency (BD). METHODS: Medical charts, urine organic acid (UOA) chromatograms, and biotinidase (BTD) enzyme activity of 113 suspected BD cases and BTD gene results of BTD enzyme deficient patients presenting at the Biochemical Genetics Clinic, AKUH from January 2010 to December 2019 were reviewed. Details were collected on a prestructured questionnaire. SPSS 22 was used for data analysis. RESULTS: BD was found in 33 (29.23%) cases, 28 being profound and 5 partial BD. The median age of BD diagnosis was 171 days (IQR: 81 - 1,022.75) and 300 days (IQR: 25 - 1,540) for the profound and partial BD, respectively. The median BTD levels in the partial BD and profound BD groups were 35 U (IQR: 25.5 - 62.5) and 15 U (IQR: 11 - 17), respectively. UOA analysis exhibited sensitivity, specificity, and agreement of 52.94%, 86.05%, and 76.67% with BTD enzyme activity. The BTD sequencing revealed seven recurrent homozygous single nucleotide variants (SNVs) and small indels. These variants include three frameshift, protein truncating variants and four missense variants. We report two novel protein truncating variants, c.929GinsA, p.S310fs*14 and c.394insA, p.T132Nfs*30 and one missense variant, c.416G>A, p.S139N that had not been reported in BD associated literature and clinical databases. CONCLUSIONS: Thirty-three cases of BD from a single center indicates a high frequency of BD in Pakistan. Late diagnosis emphasizes the need for increased clinical awareness and preferably screening for BD in this population.

Maple syrup urine disease: magnetic resonance imaging findings in three patients.

Maple syrup urine disease (MSUD) is an autosomal recessive inherited metabolic disorder, caused by branched-chain alpha-ketoacid dehydrogenase (BCKD) deficiency, leading to toxic accumulation of branched-chain amino acids (BCAAs) including leucine, isoleucine and valine and their corresponding a-ketoacids. The diagnosis of MSUD is based on elevated BCAAs and allo-isoleucine in plasma, and branched-chain hydroxyacids and ketoacids in urine. The identification of alloisoleucine >5 µmol/L is considered pathognomonic. Moreover, brain magnetic resonance imaging (MRI) showing atypical signal intensity and oedema is characteristic of MSUD. Recognition of the classical neuro-radiological findings of MSUD is particularly useful in local settings as many healthcare facilities lack the resources to measure Plasma Amino Acids (PAA). We report three cases of MSUD, in whom the disorder was strongly suspected at presentation, based on classical brain MRI findings, which was urgently confirmed by PAA analysis.

Is diagnosing patients with Organic Acidurias and Aminoacidopathies enough? Conundrums of a low middle-income country.

OBJECTIVE: This study was done to determine the factors responsible for non-treatment of inherited metabolic disorders (IMDs) requiring food for special medical purposes (FSMPs) in Pakistan. METHODS: A descriptive cross-sectional study was conducted by Departments of Pediatrics & Child Health and Pathology & Laboratory Medicine, Aga Khan University. Patients diagnosed with IMDs from January 2013 to December 2016 requiring FSMPs were surveyed after a year of initial diagnosis to collect the details of treatment advised, mortality status, and reasons of non-treatment, including not prescribed by physician, non-acceptance by family, non-availability or non-affordability. RESULTS: Over four years period, 311 patients were identified with IMDs; Median age of patients was 1.0 yrs (0.0.2-3.65) with 54% (n=168) being male. Of the total 38.2% (n=119) required FSMPs, 9% (n=28) patients were excluded due to unavailability of diagnostics information. Parents of 58 patients requiring FSMPs out of 119 participated in survey. The leading causes of non-treatment were, FSMPs not prescribed by physicians (n= 30, 51.7%) followed by non-affordability (n=23, 39.6%), families' unacceptance in (n=9, 18%) patients, non-availability of FSMPs (n=2, 3.4%) and early death of patient (n=1, 1.7%). CONCLUSION: The main factors responsible for non-treatment of FSMPs requiring IMDs were non-prescription by physician and non-affordability.

Glycogen storage diseases-time to flip the outdated diagnostic approach centered on liver biopsy with the molecular testing.

The glycogen storage diseases (GSDs) are a group of inherited metabolic disorders that result from a defect in any one of several enzymes required for either glycogen synthesis or glycogen degradation. The traditional diagnostic approach is based on the invasive hepatic or muscle biopsies, which are neither cost effective nor convenient. Molecular (gene testing) has emerged over the course of past few years as a robust alternative diagnostic tool, which not only confirms the diagnosis of GSDs but also clearly differentiates the types of GSDs allowing the initiation of the type-specific appropriate treatment for the particular type of GSDs. The aim of this update is to highlight the limitations of undertaking a liver biopsy for the diagnosis of GSDs; and to further describe the pros of the molecular testing for better patient centered care.

Retrospective Study of Patients with Hyperphenylalaninemia- Experience from a Tertiary Care Center in Pakistan.

OBJECTIVE: To assess the clinical and biochemical features as well as outcome of hyperphenylalaninemia patients. Methods: The descriptive retrospective study was conducted at the Aga Khan University Hospital, Karachi, and comprised data from January 2013 to February 2017 of plasma amino acid analysed at the Biochemical Genetic Laboratory of patients with phenylalanine levels >120 umol/L. Medical charts of patients registered with the Metabolic Clinics were reviewed, while outside referrals were contacted by telephone to collect data on a pre-structured questionnaire. Data was analysed using SPSS 21. RESULTS: Of the 18 patients, 13(72%) were males. Overall median age was 606 days (interquartile range: 761) and median phenylalanine levels were 1280 (interquartile range: 935) umol/L. Phenylalanine hydroxylase deficiency was present in 5(28%) patients while 3(16.6%) had defects in the metabolism or regeneration of tetrahydrobiopterin. The most common clinical features was intellectual deficit and seizures 14(78%) each, followed by lighter hair colour 10(55.5%) and hypotonia 11(61%). High treatment cost was the leading reason for cessation of therapy in 7(39%) followed by refusal by patient's family 5(28%). CONCLUSIONS: Most hyperphenylalaninemia cases were diagnosed late when intellectual disability had already developed.

Inherited metabolic disorders presenting as hypoxic ischaemic encephalopathy: A case series of patients presenting at a tertiary care hospital in Pakistan.

In spite of the efforts and interventions by the Government of Pakistan and The World Health Organization, the neonatal mortality in Pakistan has declined by only 0.9% as compared to the global average decline of 2.1% between 2000 and 2010. This has resulted in failure to achieve the global Millennium Development Goal 4. Hypoxic-ischaemic encephalopathy, still birth, sepsis, pneumonia, diarrhoea and birth defects are commonly attributed as leading causes of neonatal mortality in Pakistan. Inherited metabolic disorders often present at the time of birth or the first few days of life. The clinical presentation of the inherited metabolic disorders including hypotonia, seizure and lactic acidosis overlap with clinical features of hypoxic-ischaemic encephalopathy and sepsis. Thus, these disorders are often either missed or wrongly diagnosed as hypoxicischaemic encephalopathy or sepsis unless the physicians actively investigate for the underlying inherited metabolic disorders. We present 4 neonates who had received the diagnosis of hypoxic-ischaemic encephalopathy and eventually were diagnosed to have various inherited metabolic disorders. Neonates with sepsis and hypoxic-ischaemic encephalopathy-like clinical presentation should be evaluated for inherited metabolic disorders.

Diagnostic dilemma of patients with methylmalonic aciduria: Experience from a tertiary care centre in Pakistan.

OBJECTIVE: To determine the frequency of disorders leading to methylmalonic acidurias. METHODS: This cross-sectional study was conducted from January 2013 to April 2016 at the Aga Khan University Hospital, Karachi, and comprised patients diagnosed with methylmalonic acidurias based on urine organic acid analysis. Clinical history and biochemical data was collected from the biochemical genetics laboratory requisition forms. Organic acid chromatograms of all the subjects were critically reviewed by a biochemical pathologist and a metabolic physician. For assessing the clinical outcome, medical charts of the patients were reviewed. SPSS 19 was used for data analysis. RESULTS: Of the 1,778 patients 50(2.81%) were detected with methylmalonic acidurias. After excluding patients with non-significant peaks of methylmalonic acidemia, 41(2.31%) were included in the final analysis. Of these, 20(48.7%) were females, while the overall median age was 11.5 months (interquartile range: 6-41.5). On stratification by type of disorders leading to methylmalonic acidurias, 9(22%) had methylmalonic acidemia, 12(29%) had Cobalamin-related remethylation disorders, nonspecific methylmalonic acidurias in 16(39%), while 2(5%) each had succinyl coenzyme A synthetase and Vitamin B12 deficiency. respectively. CONCLUSIONS: Screening tests, including urine organic acid, provided valuable clues to the aetiology of methylmalonic acidurias.

Ethical issues in managing Lysosomal storage disorders in children in low and middle income countries.

The lysosomal storage diseases are a group of rare, inherited metabolic diseases affecting about 1 in 7000 to 8000 people. In recent years, the introduction of enzyme replacement therapy, substrate reduction therapy and small molecule therapy, has changed the natural course of this otherwise progressive group of disorders leading to severe morbidity and early mortality. These treatment options, however, are extremely expensive and are needed for life thus presenting an economical as well as ethical challenge to the affected families and the health care system of a country. This paper presents a case for the prevention of the lysosomal storage disorders as a model for other inherited metabolic disorders in the form of antenatal testing and cascade screeningfor couples and families at risk of having affected off-springs and compares it to the cost incurred on the enzyme replacement therapy in the backdrop of the health care prioritiesof Pakistan, a low middle income country. Similar economic and ethical challenges are faced by most low and middle income countries. The literature search was done using Pubmed and Clinical trials databases using key words: "Lysosomal storage disorders", "natural course", "ethics", "cascade screening", "Thalassemia" and "cascade screening". A total of 225 articles in English language were scanned from 1980-2016, 80 articles describing the natural course of LSD with and without ERT, ethical issues related to the treatment of LSD and strategies employed for the prevention of genetic disorders were prioritized.

Pre-natal genetic counseling in a resource limited country--a single center geneticist's perspectives.

OBJECTIVE: To assess the needs related to prenatal genetic counselling in a developing country. METHODS: The prospective observational study was conducted at the Prenatal-Genetic Counselling Clinic of Aga Khan University Hospital, Karachi, from October 2007 to September 2010. In-depth interviews were conducted and the data was stored in the form of patient charts. Information was then extracted from the charts and entered into a structured questionnaire. RESULTS: Of the 93 couples in the study, 49 (53%) were in the self-referral group and 44 (47%) were in the physician- referral group. Diagnosis was not given for previously affected children by the paediatrician or by obstetrician for recurrent miscarriages in 68 (73%)cases. Besides, 20 (22%) couples had voluntarily terminated a pregnancy without any tests because of the fear of having a diseased child. Eleven (12%) couples were looking for amniocentensis or chorionic villus sampling. Death in previous children was the main reason to seek genetic counselling and was seen in 57 (61%) couples. Consanguinity was seen in 77 (83%) couples. CONCLUSION: A clear deficiency of knowledge of genetics was seen among the non-genetic healthcare providers. Demand of antenatal genetic testing among the public was also seen, highlighting the need of diagnostic facility for genetic and metabolic disorders. However, this needs to be explored in the context of the existing healthcare infrastructure.

Glutaric aciduria type 1--importance of early diagnosis and treatment.

Glutaric aciduria type 1 is a rare inherited organic academia. Untreated patients characteristically develop dystonia secondary to striatal injury during early childhood, which results in high morbidity and mortality. In patients diagnosed during neonatal period, striatal injury can be prevented by metabolic treatment including low lysine diet, carnitine supplementation and aggressive emergency treatment during acute episode of inter current illnesses. However, after the onset of neurological damage initiation of treatment is generally not effective. Therefore; glutaric aciduria type 1 is included in newborn screening panel for inherited metabolic diseases in many countries. We describe two children in a family with glutaric aciduria type 1 and their different long term outcomes. The first child was diagnosed late leading to severe neurological damage. The second child was diagnosed in the neonatal period as a result of selective high-risk screening and was treated appropriately giving a normal growth.