Multi-gene testing in neurological disorders showed an improved diagnostic yield: data from over 1000 Indian patients

BACKGROUND

Neurological disorders are clinically heterogeneous group of disorders and are major causes of disability and death. Several of these disorders are caused due to genetic aberration. A precise and confirmatory diagnosis in the patients in a timely manner is essential for appropriate therapeutic and management strategies. Due to the complexity of the clinical presentations across various neurological disorders, arriving at an accurate diagnosis remains a challenge.

METHODS

We sequenced 1012 unrelated patients from India with suspected neurological disorders, using TruSight One panel. Genetic variations were identified using the Strand NGS software and interpreted using the StrandOmics platform.

RESULTS

We were able to detect mutations in 197 genes in 405 (40%) cases and 178 mutations were novel. The highest diagnostic rate was observed among patients with muscular dystrophy (64%) followed by leukodystrophy and ataxia (43%, each). In our cohort, 26% of the patients who received definitive diagnosis were primarily referred with complex neurological phenotypes with no suggestive diagnosis. In terms of mutations types, 62.8% were truncating and in addition, 13.4% were structural variants, which are also likely to cause loss of function.

CONCLUSION

In our study, we observed an improved performance of multi-gene panel testing, with an overall diagnostic yield of 40%. Furthermore, we show that NGS (next-generation sequencing)-based testing is comprehensive and can detect all types of variants including structural variants. It can be considered as a single-platform genetic test for neurological disorders that can provide a swift and definitive diagnosis in a cost-effective manner.

Novel mutations in SERAC1 gene in two Indian patients presenting with dystonia and intellectual disability

In this study we present the first two cases from India of a rare inborn error of metabolism manifesting as dystonia and 3-methylglutaconic aciduria and a Leigh like lesions in the brain MRI associated with SERAC1 gene mutation, a phenotype characteristic of MEGDEL syndrome. A four base pair duplication in exon 15 i.e.NM_032861.3 (SERAC1) c. 1643_1646 dup ATCT (p.(Leu550SerfsX19)) and another with a homozygous missense variation in exon 15 i.e. NM_032861.3 (SERAC1) c.1709 G > A (p.(Gly526Glu)) were detected and both were novel mutations. Hepatopathy was observed in the neonatal period with lactic acidosis in one child and at the age of 5yrs in the other. These cases add to the existing number of patients identified till today and additional mutations in the SERAC1 gene.

Spectrum of mutations in Glutaryl-CoA dehydrogenase gene in glutaric aciduria type I--Study from South India

BACKGROUND

Glutaric aciduria type I is an autosomal recessive organic acid disorder. The primary defect is the deficiency of Glutaryl-CoA dehydrogenase (EC number 1.3.99.7) enzyme that is involved in the catabolic pathways of the amino acids l-lysine, l-hydroxylysine, and l-tryptophan. It is a treatable neuro-metabolic disorder. Early diagnosis and treatment helps in preventing brain damage.

METHODS

The Glutaryl-CoA dehydrogenase gene (GCDH) gene was sequenced to identify disease causing mutations by direct sequencing of all the exons in twelve patients who were biochemically confirmed with GA I.

RESULTS

We identified eleven mutations of which nine are homozygous mutations, one heterozygous and two synonymous mutations. Among the eleven mutations, four mutations p.Q162R, p.P286S, p.W225X in two families and p.V410M are novel. A milder clinical presentation is observed in those families who are either heterozygous or with a benign synonymous SNP. Multiple sequence alignment (MSA) of GCDH with its homologues revealed that the observed novel mutations are not tolerated by protein structure and function.

CONCLUSIONS

The present study indicates genetic heterogeneity in GCDH gene mutations among South Indian population. Genetic analysis is useful in prenatal diagnosis and prevention. Mutation analysis is a useful tool in the absence of non-availability of enzyme assay in GA I.

GALNS mutations in Indian patients with mucopolysaccharidosis IVA

Mucopolysaccharidosis IV A (Morquio syndrome A, MPS IVA) is a lysosomal storage disease caused by the deficiency of N-acetylgalactosamine-6-sulfatase (GALNS). The mutation spectrum in this condition is yet to be determined in Indians. We aimed to analyze the mutations in the GALNS gene in Asian Indians with MPS IVA. All the exons and the adjacent intronic regions of the gene were amplified and sequenced in sixty-eight unrelated Indian families. We identified 136 mutant alleles comprising of 40 different mutations. We report twenty-two novel mutations that comprise of seventeen missense (p.Asn32Thr, p.Leu36Arg, p.Pro52Leu, p.Pro77Ser, p.Cys79Arg, p.His142Pro, p.Tyr191Asp, p.Asn204Thr, p.Gly188Ser, p.Phe216Ser, p.Trp230Cys, p.Ala291Ser, p.Gly317Arg, p.His329Pro, p.Arg386Ser, p.Glu450Gly, p.Cys501Ser), three splice-site variants (c.120+1G>C, c.1003-3C>G, c.1139+1G>A), one nonsense mutation (p.Gln414*) and one frameshift mutation (p.Pro420Leufs*440). Eighteen mutations have been reported earlier. Among these p.Ser287Leu (8.82%), p.Phe216Ser (7.35%), p.Asn32Thr (6.61%) and p.Ala291Ser (5.88%) were the most frequent mutations in Indian patients but were rare in the mutational profiles reported in other populations. These results indicate that the Indian patients may have a distinct mutation spectrum compared to those of other populations. Mutant alleles in exon 1, 7 and 8 accounted for 44.8% of the mutations, and sequencing of these exons initially may be a cost-effective approach in Asian Indian patients. This is the largest study on molecular analysis of patients with MPS IVA reported in the literature, and the first report from India.

Ring Chromosome 20 Associated with Refractory Epilepsy: A Case Report

Ring chromosome 20 is a rare chromosomal abnormality characterized mainly by refractory epileptic seizures, cognitive and behavioral problems, and absence of definite dysmorphic features. We report a 5-year-old boy with refractory epilepsy and minimal dysmorphic features who first presented with mild developmental delay at 11 months of age. The karyotype of the child was 46,XY,r(20)(p13q13.3). Till date there are 69 cases of ring chromosome 20 reported in the literature, including mosaics and supernumerary ring chromosomes. To our knowledge, this is the first case of ring chromosome 20 with refractory epilepsy reported from the south Indian population.DOI: http://dx.doi.org/10.3126/ajms.v2i3.5607Asian Journal of Medical Sciences 2 (2011) 141-144

Phenylalanine hydroxylase gene mutations in phenylketonuria patients from India: identification of novel mutations that affect PAH RNA

Analysis of seven Indian phenylketonuria families has revealed four novel mutations in the phenylalanine hydroxylase gene; two affected consensus splice sequence and the 3' UTR, respectively, while the other two were single base insertion and deletion mutations, respectively. A novel 3' splice site mutation c.168-2A>G resulted in the activation of a cryptic 3' splice site that generated a premature termination codon leading to very low levels of the mutant transcript, probably due to activation of the nonsense-mediated decay (NMD) pathway. This is probably the first report of PKU caused by the activation of NMD.

Hyperhomocysteinemia and the compound heterozygous state for methylene tetrahydrofolate reductase are independent risk factors for deep vein thrombosis among South Indians

To investigate the role of methylene tetrahydrofolate reductase (MTHFR) (677 C-->T and 1298 A-->C), factor V (1691 G-->A), factor II (20210 G-->A) genetic polymorphisms and hyperhomocysteinemia in the aetiology of deep vein thrombosis (DVT) in 163 cases and 163 controls. Polymerase chain reaction-restriction fragment length polymorphism was used for genotyping, reverse-phase high-performance liquid chromatography for plasma homocysteine, and Student's t-test and Fisher exact tests were used for statistical analysis. Elevated mean plasma homocysteine levels were observed in DVT cases irrespective of gender differences. Homocysteine elevation above the 95th percentile of the control group associated with 9.4-fold and 7.6-fold increased risk for DVT in men and women, respectively. Genotyping showed the MTHFR 677CT/1298AC genotype (i.e. compound heterozygosity) is associated with 3.5-fold risk for thrombosis. The factor V Leiden mutation frequency was higher in DVT cases, but not statistically significant; however, genetic predisposition to this mutation was associated with early age of DVT onset. Factor II mutation was absent in cases and controls. Co-segregation of two or more risk factors was associated with 11.7-fold increased risk for thrombosis. This study projects that hyperhomocysteinemia and compound heterozygous state for MTHFR are independent risk factors for DVT among South Indians.

Evaluation of total plasma homocysteine in Indian newborns using heel-prick samples

OBJECTIVE

To estimate total plasma homocysteine levels in Indian newborns by modifying the existing SBD-F based High performance liquid chromotography (HPLC) method in order to enable analysis in newborn heel-prick samples and assess the prevalence of hyperhomocysteinemia in Indian newborns who are exclusively breast-fed.

METHODS

Reverse-phase HPLC with fluorescence detection for plasma homocysteine estimation and statistical analysis using student t-test.

RESULTS

SBD-F based HPLC method was modified and Bland and Altman analysis was carried out to assess agreement between original and modified methods. The correlation co-efficient was 0.994. The limits of agreement (-5.9, 6.3) were small enough to apply new method in place of the old for heel-prick sample analysis. Total plasma homocysteine analysis was carried out on heel-prick samples of 607 randomly selected newborns (331 males and 276 females). The mean plasma homocysteine estimated by this method in Indian newborns was 6.99 (95% CI: 6.48-7.49) with no appreciable gender effect (P=0.74). Elevated homocysteine levels were observed in 31 males and 21 females.

CONCLUSIONS

Modified HPLC method is validated and can be used for homocysteine analysis on newborn heel-prick samples. Using this method, the prevalence of hyperhomocysteinemia in Indian newborns is 8.6%.

Newborn screening in India

Expanded newborn screening (NBS) is aimed for early detection and intervention of treatable inborn errors of metabolism and also to establish incidence of these disorders in this part of the globe. The first expanded NBS programme initiated in the capital city of Andhra Pradesh to screen all the newborns born in four major Government Maternity Hospitals in Hyderabad by heel prick capillary blood collected on S&S 903 filter paper. Chromatographic (TLC and HPLC), electrophoretic (cellulose acetate and agarose) and ELISA based assays have been employed for screening of common inborn errors of metabolism. This study has shown a high prevalence of treatable Inborn errors of metabolism. Congenital hypothyroidsm is the most common disorder (1 in 1700) followed by congenital Adrenal Hyperplasia (1 in 2575) and Hyperhomocystenemia (1 in 100). Interestingly, a very high prevalence of inborn errors of metabolism to the extent of 1 in every thousand newborns was observed. The study reveals the importance of screening in India, necessitating nation wide large-scale screening.