Development, validation and application of single molecule molecular inversion probe based novel integrated genetic screening method for 29 common lysosomal storage disorders in India.

BACKGROUND: Current clinical diagnosis pathway for lysosomal storage disorders (LSDs) involves sequential biochemical enzymatic tests followed by DNA sequencing, which is iterative, has low diagnostic yield and is costly due to overlapping clinical presentations. Here, we describe a novel low-cost and high-throughput sequencing assay using single-molecule molecular inversion probes (smMIPs) to screen for causative single nucleotide variants (SNVs) and copy number variants (CNVs) in genes associated with 29 common LSDs in India. RESULTS: 903 smMIPs were designed to target exon and exon-intron boundaries of targeted genes (n = 23; 53.7 kb of the human genome) and were equimolarly pooled to create a sequencing library. After extensive validation in a cohort of 50 patients, we screened 300 patients with either biochemical diagnosis (n = 187) or clinical suspicion (n = 113) of LSDs. A diagnostic yield of 83.4% was observed in patients with prior biochemical diagnosis of LSD. Furthermore, diagnostic yield of 73.9% (n = 54/73) was observed in patients with high clinical suspicion of LSD in contrast with 2.4% (n = 1/40) in patients with low clinical suspicion of LSD. In addition to detecting SNVs, the assay could detect single and multi-exon copy number variants with high confidence. Critically, Niemann-Pick disease type C and neuronal ceroid lipofuscinosis-6 diseases for which biochemical testing is unavailable, could be diagnosed using our assay. Lastly, we observed a non-inferior performance of the assay in DNA extracted from dried blood spots in comparison with whole blood. CONCLUSION: We developed a flexible and scalable assay to reliably detect genetic causes of 29 common LSDs in India. The assay consolidates the detection of multiple variant types in multiple sample types while having improved diagnostic yield at same or lower cost compared to current clinical paradigm.

Extending the Phenotype and Identification of a Novel Candidate Gene for Immunodeficiency in 5q11 Microdeletion Syndrome.

Array CGH has led to the delineation of innumerable microdeletion syndromes. We present a patient with a 7-Mb deletion at 5q11.2 with previously unreported features, such as immunodeficiency, asymmetry of hands and feet, joint laxity, and agenesis of corpus callosum. The clinical features of this patient are compared with 13 patients reported previously. A common critical region (CCR) of 1.4 Mb (54-55.4 Mb) is defined in all cases including the present one. Of the 14 genes present in CCR, IL6ST is proposed to be the candidate gene for immunodeficiency observed in some of these patients. IL6ST encodes gp130, a signal transduction protein for various interleukins and cytokines. It is involved in the generation of both T and B lymphocytes as well as the production of acute-phase reactants. Microdeletion 5q11.2 should be considered as a recognisable syndrome based on the common phenotype and the novel features described.

Inherited metabolic disorders: prenatal diagnosis of lysosomal storage disorders.

OBJECTIVE: To offer accurate prenatal diagnosis of lysosomal storage disorders in early pregnancy. METHOD: Prenatal enzymatic diagnoses of Gaucher, Fabry, Pompe, Niemann Pick A/B, Tay Sach, Sandoff, GM1, mucoplysaccharidoses, Wolman, Krabbe, Metachromatic leukodystrophy and Batten diseases were made in uncultured chorionic villi samples by fluorometric/spectrophotometric methods. RESULTS: Of 331 prenatal enzymatic diagnosis, 207 fetuses (67%) were normal and 124 (37%) were affected. The interpretation of affected, normal and carrier fetuses was done using their respective reference ranges as well as % enzyme activity of normal mean. The prenatal molecular confirmation was feasible in 43 biochemically diagnosed fetuses. Of the 207 normal reported fetuses, post natal enzymatic confirmation was done in 23 babies, clinical status of another 165 babies was assessed as unaffected via questionnaire on telephone and 19 were lost to follow-up. In affected pregnancies, 123 opted for termination of which 44 were confirmed enzymatically after abortion. A single false positive was determined to be a carrier by prenatal mutation analysis and carried to term. CONCLUSION: We recommend uncultured chorionic villi for reliable prenatal enzymatic diagnosis of various lysosomal storage disorders on account of the low rate of false positive (0.5%) and false negative (2.2%) results.

Fanconi-Bickel syndrome - mutation in SLC2A2 gene.

Fanconi-Bickel Syndrome (FBS) is a rare autosomal recessive disorder of carbohydrate metabolism. The defect in the GLUT 2 receptors in the hepatocytes, pancreas and renal tubules leads to symptoms secondary to glycogen storage, glucose metabolism and renal tubular dysfunction. Derangement in glucose metabolism is classical with fasting hypoglycemia and post-prandial hyperglycemia. The authors report a 4-year-old boy who presented with failure to thrive, motor delay, protuberant abdomen and was noted to have huge hepatomegaly with glycogen deposition in liver, and renal tubular acidosis. Gene sequencing revealed homozygous mutation, c.1330T > C in SLC2A2 gene, thus confirming the diagnosis of FBS. Only three mutations have been reported from India so far. The primary reason for referral to authors' hospital was for liver transplantation, but an accurate diagnosis led to avoidance of the major surgery and streamlining of treatment with clinical benefit to the child and family.

Exome sequencing reveals SCO2 mutations in a family presented with fatal infantile hyperthermia.

We applied whole-exome sequencing (WES) for identification of an underlying genetic cause of a disease in a family presented with fatal infantile hyperthermia. Analysis of WES results revealed novel, deleterious compound missense mutations, Val160Ala and Pro233Thr, in the synthesis of cytochrome C oxidase 2 gene (SCO2) encoding a mitochondrial protein, Sco2, which is important for cytochrome C oxidase (COX) synthesis. Autosomal recessive mutations in SCO2 are known to be associated with COX deficiency recognized as fatal infantile cardio-encephalomyopathy (604272, OMIM). The Val160Ala and Pro233Thr mutations occurred in the conserved thioredoxin domain of Sco2 and predicted to disrupt protein folding and interaction of Sco2 with other proteins. Our results show applicability of WES in identification of disease-causing mutations and in establishing molecular diagnosis of severe, infantile onset disorder with a challenging diagnosis.

Molecular characterisation and prenatal diagnosis of Asparto-acylase deficiency (Canavan disease)--report of two novel and two known mutations from the Indian subcontinent.

OBJECTIVES: To establish a technique for mutation identification and prenatal screening in confirmed cases of Canavan disease. METHOD: Mutations in ASPA gene were identified by sequencing. Six exons of ASPA gene were amplified using intronic primers flanking the exons and then sequenced on ABI 3500Dx automated unit. This technique was used to identify mutations in three cases of Canavan disease. Prenatal diagnosis was performed in two families. RESULTS: Two reported mutations c.162 C > A (p.Asn54Lys) and c.859 G > A (p.Ala287Thr) were identified in two different cases of Canavan disease. Third case was compound heterozygous for two novel mutations (c.728 T > G, p.Ile243Ser; c.902 T > C, p.Leu301Pro). Prenatal diagnosis was performed in three pregnancies in two families, two affected fetuses and one unaffected fetus were identified. CONCLUSIONS: Molecular characterization of Canavan disease helps identify the cause at genetic level, thus confirming diagnosis and enabling identification of carriers in the family. Though enzyme assay and NAA measurement allows diagnosis and prenatal diagnosis of Canavan diasease, molecular methods have the advantage of bringing accuracy in prenatal testing with an earlier result. This is the first case report of mutation studies in Canavan disease from Indian subcontinent.

Mutation analysis of the CFTR gene in 225 children: identification of five novel severe and seven reported severe mutations.

BACKGROUND: Cystic fibrosis (CF) is the most common inherited disorder in Caucasian populations, with more than 1400 cystic fibrosis transmembrane conductance regulator (CFTR) gene mutations. The type of mutations and their distributions varies widely between different countries and/or ethnic groups. METHODS: We characterized the mutations in the CFTR gene by single-strand conformation polymorphism followed by sequencing in CF patients. RESULTS: Twelve mutations were found in 79/225 (35.1%) patients. The most frequent mutations were F508 deletion (31.1%), p.R1162× (2.2%), p.M1T (0.8%), and S559N (0.8%). Five novel severe mutations (p.R80N11fs*11, p.R75G, p.Y577×, p.Y808Yfs*10, and p.I331×) and three reported mutations (p.C343×, p.Ile1000×, p.M469V) were detected. CONCLUSION: The protocol for identification of mutations in cases of CF in developing countries would have to include a different set of mutations than those reported from western countries.

Newborn screening for congenital hypothyroidism in very-low-birth-weight babies: the need for a second test.

BACKGROUND: Very-low-birth-weight babies (VLBW) with hypothyroidism may show a delayed postnatal rise in thyroid stimulating hormone (TSH), mainly due to immaturity of the hypothalamic-pituitary-thyroid axis. Transient hypothyroidism is prevalent in VLBW babies and some affected babies are considered to need treatment. There is disagreement about whether a second screening test is needed in VLBW babies to detect all cases that need treatment. METHODS: We included in the study all babies with a birth weight ≤ 1,500 g born in New South Wales and the Australian Capital Territory between January 2006 and December 2008. Newborn screening samples for TSH measurement were taken in the first days of life and again at 1 month. During week 1, a blood-spot TSH level of ≥20 mIU/L was considered positive, and at 1 month a positive level was ≥7 mIU/L, and triggered full investigation. RESULTS: In the cohort of 301,000 babies, 2,313 VLBW babies survived for testing, and 2,117 repeat screening samples were received. Forty-three babies had transient hypothyroidism, with thyroid function normalising before 2 months of age, usually without treatment. Eighteen babies required treatment beyond 2 months of age (1:128 of surviving babies), 16 having had normal TSH results on initial testing, and 12 having levels below 6 mIU/L. CONCLUSION: Significant hypothyroidism, transient or permanent, but persisting beyond 2 months of age is common in VLBW babies. There is a delayed rise in TSH in some, and secondary screening at 1 month of age detects babies deemed by local paediatric endocrinologists as needing treatment.

Mutation studies in X-linked myotubular myopathy in three Indian families.

Congenital myopathies are a group of genetic disorders characterized by generalised muscle hypotonia and weakness of varying severity. They are distinct entities and do not include muscular dystrophies, metabolic myopathies and mitochondrial disorders. Myotubular myopathy is a rare sub type within this group of disorders. Clinical differentiation of the various types is difficult and requires muscle biopsy with histopathological and immunohistochemical studies for specific diagnosis. Gene studies are a prerequisite for genetic counseling adn prenatal diagnosis. Here presented three cases of X-linked myotubular myopathy in three Indian families where the diagnosis was established by mutation analysis in the MTM1 gene in all, and supported his histopathology in two. All three families had history of previous male neonatal deaths with similar complaints. Molecular analysis revealed hemizygous mutations in the MTM1 gene including c.1261-10A>G in case, 1, c.70C>T (R24X) in case 2, and a previously unreported mutation, c.924_926delCTT(p. F308del), in case 3. Genetic counseling was performed regarding the X-linked inheritance, their 50% risk of recurrence in boys in subsequent pregnancies, and a feasibility of prenatal diagnosis. This is the first report of cases of X-linked myotubular myopathy from India.

Combined enzyme replacement and haematopoietic stem cell transplantation in Hurler syndrome.

We report the long-term follow-up of successful treatment of mucopolysaccharidosis type I H (MPS IH, Hurler syndrome) with combined enzyme replacement therapy and haematopoietic progenitor stem cell transplant.

Tyrosinemia type I--diagnostic issues and prenatal diagnosis.

A fifteen-month-old boy, born to consanguineously married couple, presented with asymptomatic hepatomegaly. Investigations revealed mildly deranged liver functions, necroinflammatory changes and cirrhosis on liver biopsy, a markedly raised alpha feto protein and tyrosine levels in plasma and a generalized aminoaciduria. His diagnosis of hereditary tyrosinemia was established on findings of raised serum and urine succinylacetone and a deficient activity of fumaryl acetoacetate hydroxylase enzyme. Prenatal diagnosis of hereditary tyrosinemia was performed in a subsequent pregnancy in this family from India.

Leber's hereditary optic neuropathy with molecular characterization in two Indian families.

PURPOSE: Leber's hereditary optic neuropathy (LHON) presents in early adulthood with painless progressive blindness of one or both eyes. Usually there is a positive family history of similar disease on the maternal side. Definitive diagnosis can be established by finding the change in the mitochondrial gene. No molecular studies have been reported from India. MATERIAL AND METHODS: Clinical, ophthalmologic and molecular studies were carried out in two patients from different families and available first degree relatives. The subjects were tested for the three common mutations seen in LHON by molecular techniques of polymerase chain reaction using mutation specific primers. RESULTS: The mutations G3460A and G11778A in the mitochondrial genes MTND1 and MTND4, known to be causative for LHON, were found in one family each. CONCLUSION: Diagnosis of LHON should be considered in familial cases and in young adults with optic atrophy. Confirmation of diagnosis should be sought by molecular gene analysis. Genetic counselling should be offered to all 'at risk' relatives of a patient harbouring the mutation.

Gerodermia Osteodysplastica.

Gerodermia Osteodysplastica is a rare autosomal recessive connective tissue disorder included in the cutis laxa syndromes. Twenty five cases have been reported in the world literature to date. The authors report the first case from our country, a 13 year old female having phenotypic and radiological features suggestive of this genetic disorder.

Genetic counseling and prenatal diagnosis in India--experience at Sir Ganga Ram Hospital.

UNLABELLED: The experiences in genetic counseling and prenatal diagnosis at a tertiary genetic center in India are described. Of 3500 subjects provided genetic counseling 28.7% were for prenatal diagnosis, 13.7% for mental retardation +/- malformations, 11.5% for thalassemia, hemophilia and leukemia, 8.5% for neural tube defects and other malformations, and 8% for muscle dystrophy and spinal muscle atrophy. Chromosomal studies in blood (n = 5459) were for recurrent abortions (57.8%), delayed milestones (14.7%), malformations (11%), and infertility and amenorrhea (10.2%). Indications for amniotic fluid studies (n = 835) were advanced maternal age (35.7%), high risk result on triple test (21.3%), previous child with trisomy 21 (21.3%) and abnormalities seen on ultrasound (11.1%). Molecular studies were mostly for thalassemia (843, 24.3%), Duchenne muscular dystrophy (443, 12.5%), fragile X syndrome (367, 10.3%), spinal muscular atrophy (315, 8.9%), thrombophilia profile (233, 6.6%), triplet repeat disorders-spinocerebellar ataxias, Huntington disease and Friedreich ataxia-162 (4.6%), cystic fibrosis 140 (3.9%) and mitochondrial disorders 101 (2.9%). Other disorders for which molecular diagnosis was done were intrauterine infections by PCR on the amniotic fluid, Prader Willi/Angelman syndromes, hemophilia, achondroplasia, congenital adrenal hyperplasia, and Apert syndrome etc. In biochemical studies triple marker tests were the most common (3239), followed by aminoacid chromatography (774). Among neurolipidosis metachromatic leukodystrophy was the commonest, followed by Krabbe's disease, Tay Sach disease and Gaucher disease. Of the mucopolysacharidoses Hurler syndrome was the commonest, followed by Hunter syndrome. These data are compared with previous studies and a change towards increased prenatal diagnostic tests is observed. The commonest indication for amniocentesis has changed to advanced maternal age. CONCLUSION: Advanced molecular, cytogenetic and biochemical techniques have been a useful addition for genetic counseling and prenatal diagnosis in India.

Triple A syndrome--diagnostic and management issues.

The authors present a family with three children affected with triple A syndrome--one had died, one was saved by diagnosis and timely therapy, and one was born after the diagnosis in the second child. The gene for the syndrome has been cloned and genetic counseling should be offered to these families.

Genetic counseling in acrocallosal syndrome.

This article reports two families with children having acrocallosal syndrome, an autosomal recessive disorder characterized by agenesis of corpus callosum, facial dysmorphism and polydactyly along with psychomotor retardation. Both families sought genetic counseling in subsequent pregnancies. Although the gene for the disorder is not yet identified, prenatal diagnosis was attempted by ultrasound studies. In both families, an affected fetus was diagnosed in the presence of postaxial polydactyly of hands and absence of corpus callosum. It is emphasized that pediatricians should make precise diagnosis in cases of dysmorphism and mental retardation, as this enable prenatal diagnosis in future pregnancies.