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Abstract Background Rare disorders comprise of ~ 7500 different conditions affecting multiple systems. Diagnosis of rare diseases is complex due to dearth of specialized medical professionals, testing labs and limited therapeutic options. There is scarcity of data on the prevalence of rare diseases in different populations. India being home to a large population comprising of 4600 population groups, of which several thousand are endogamous, is likely to have a high burden of rare diseases. The present study provides a retrospective overview of a cohort of patients with rare genetic diseases identified at a tertiary genetic test centre in India. Results Overall, 3294 patients with 305 rare diseases were identified in the present study cohort. These were categorized into 14 disease groups based on the major organ/ organ system affected. Highest number of rare diseases (D = 149/305, 48.9%) were identified in the neuromuscular and neurodevelopmental (NMND) group followed by inborn errors of metabolism (IEM) (D = 47/305; 15.4%). Majority patients in the present cohort (N = 1992, 61%) were diagnosed under IEM group, of which Gaucher disease constituted maximum cases (N = 224, 11.2%). Under the NMND group, Duchenne muscular dystrophy (N = 291/885, 32.9%), trinucleotide repeat expansion disorders (N = 242/885; 27.3%) and spinal muscular atrophy (N = 141/885, 15.9%) were the most common. Majority cases of β-thalassemia (N = 120/149, 80.5%) and cystic fibrosis (N = 74/75, 98.7%) under the haematological and pulmonary groups were observed, respectively. Founder variants were identified for Tay-Sachs disease and mucopolysaccharidosis IVA diseases. Recurrent variants for Gaucher disease (GBA:c.1448T > C), β-thalassemia (HBB:c.92.+5G > C), non-syndromic hearing loss (GJB2:c.71G > A), albinism (TYR:c.832 C > T), congenital adrenal hyperplasia (CYP21A2:c.29–13 C > G) and progressive pseudo rheumatoid dysplasia (CCN6:c.298T > A) were observed in the present study. Conclusion The present retrospective study of rare disease patients diagnosed at a tertiary genetic test centre provides first insight into the distribution of rare genetic diseases across the country. This information will likely aid in drafting future health policies, including newborn screening programs, development of target specific panel for affordable diagnosis of rare diseases and eventually build a platform for devising novel treatment strategies for rare diseases.

Abstract 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.

Skeletal dysplasias or osteochondrodysplasias comprise a large heterogeneous group of genetic disorders and possess significant overlap on imaging, which adds to the dilemma of the reporting radiologist. These entities are routinely evaluated with a detailed skeletal survey and hand radiographs form a crucial part of a complete survey. Certain conditions have characteristic imaging findings that enable a diagnosis be made on hand radiograph alone. Additionally, hand radiographs may also demonstrate findings that may be suggestive of a particular diagnosis/differential diagnoses and would warrant further assessment for proving the same. We aim to demonstrate the use of hand radiographs in diagnosis of various such entities through this review. Although they cannot replace a complete skeletal survey in the diagnosis, hand radiographs performed for other indications might alert a radiologist to the diagnosis of an unsuspected skeletal dysplasia.

Background Structured reporting has the advantages of reducing ambiguity in written radiology reports with greater uniformity and comparability of reports amongst different institutes. It has multiple facets: structured format, structured content, and standardized language. While structured reporting initiative has been used in various radiology subspecialties such as oncology, cardiothoracic, abdominal and interventional radiology; skeletal dysplasia is a domain that remains largely untouched by this concept. Purpose To evaluate the impact of structured reporting in skeletal dysplasia. Methods and Materials This was an ethically approved pragmatic clinical trial. A defined number (75) of clinically diagnosed and/or genetically confirmed skeletal dysplasia radiographs were evaluated by two radiologists (reader A and reader B) with 5-and 7-years' experience in general radiology, respectively. A pre-defined structured reporting format for skeletal dysplasia was used as an interventional tool. Both the readers interpreted the radiographs before and after the training session. In addition to diagnosis, diagnostic confidence was noted using a semiquantitative scale. Improvement in diagnostic accuracy and diagnostic confidence after training were assessed. McNemar's test was used to assess the statistical significance of difference in proportion of correct diagnoses in pre- and post-education phases. An interrater reliability analysis using the Kappa statistic was performed to determine interobserver agreement between readers both in pre- and post-education phases. Results In the post-education phase, the proportion of accurate diagnosis improved from 48% (36/75) to 64% (48/75) for reader A, and from 44% (33/75) to 60% (45/75) for reader B as compared with the pre-education phase. Amongst the cases with a correct radiologic diagnosis, an increase in diagnostic confidence was noted in 18 cases for reader A, and 15 cases for reader B. In none of the cases, there was a reduction in diagnostic confidence after training. A McNemar's test determined that there was a statistically significant difference in the proportion of correct diagnoses in pre- and post-education phases, p

Individuals with genetic disorders present with multisystem, complex, and special health care needs. Although limited treatment options are available for most genetic conditions, ensuring continued ongoing surveillance and rehabilitative care is quintessential for improving their quality of life. Delivering comprehensive health-care directed at periodic surveillance, timely diagnosis, and specialized management of these individuals warrants ongoing evaluation and management by specialists in multiple disciplines. Multidisciplinary team approach involving coordinated care among various specialties with a patient-centric outlook ensures efficient resource utilization and cost-effective management. The establishment of “one-stop” multidisciplinary specialized clinics providing comprehensive care is expected to improve the quality of patient care and reduce the overall burden on the family.

Purpose: To report a case of diffuse xanthogranuloma presenting as bilateral anterior uveitis in a neonate. Observations: A neonate was brought by the parents with complaints of redness, watering, and photophobia in both eyes for 10 days. Examination under anesthesia revealed the presence of bilateral hyphema, fibrinous membrane, corneal haze, and raised intraocular pressure (IOP). Ultrasound Biomicroscopy revealed diffuse bilateral iris thickening. The child was managed medically with topical glaucoma medications, topical steroids, and cycloplegics. The child responded well with the resolution of hyphema, anterior chamber inflammation, and reduction of IOP. Conclusion and importance: In neonates and infants presenting with bilateral uveitis, spontaneous hyphema, and secondary glaucoma, even in the absence of a well-defined iris lesion, diffuse juvenile xanthogranuloma should be considered as a differential diagnosis.

Abstract Background Von Hippel–Lindau (VHL) syndrome is a familial cancer syndrome caused by mutations in VHL gene. It is characterized by the formation of benign and malignant tumors like retinal angioma, cerebellar hemangioblastoma, spinal hemangioblastoma, renal cell carcinoma, pheochromocytoma, pancreatic and renal cysts, and endolymphatic sac tumors. Germline mutations in VHL gene have also been reported in isolated VHL-associated tumors. VHL gene is a small gene with 3 coding exons and can be easily tested even in a resource constraint setting. Objective To describe clinical presentation and estimate the diagnostic yield of in VHL and VHL-associated tumors. Methods This is a descriptive study in a hospital setting. Here, we describe the clinical and molecular data of 69 patients with suspected VHL or having VHL-associated tumors. Sanger sequencing of coding sequences and conserved splice sites of VHL gene were done in all patients. Multiplex ligation-dependent probe amplification (MLPA) of VHL gene to detect large deletions/duplications was performed for 18 patients with no pathogenic sequence variations. Results Among tumor types at presentation, pheochromocytoma was seen in 49% (34/69), hemangioblastoma was seen in 30% (21/69), and renal cell carcinoma was seen in 7% (5/69). Rest had other tumors like paraganglioma, endolymphatic sac papillary tumors, cerebellar astrocytoma and pancreatic cyst. Seven patients (10%) had more than one tumor at the time of diagnosis. Pathogenic variations in VHL gene were identified in 31probands by Sanger sequencing; 18 were missense, 2 nonsense and 2 small indels. A heterozygous deletion of exon 3 was detected by MLPA in one patient among 18 patients for whom MLPA was done. Overall, the molecular yield was 46% cases (32/69). Family history was present in 7 mutation positive cases (22%). Overall, 11 families (16%) opted for pre-symptomatic mutation testing in the family. Conclusions Mutation testing is indicated in VHL and VHL-associated tumors. The testing facility is easy and can be adopted easily in developing countries like India. The yield is good, and with fairly high incidence of familial cases, molecular testing can help in pre-symptomatic testing and surveillance.

Abstract Fabry disease (FD) is a treatable X linked lysosomal storage disorder with a wide phenotypic spectrum. There is a scarcity of published data on the burden of FD in India. This study evaluates the clinical and molecular spectrum of Indian patients with FD. In this multicentric study involving 10 tertiary referral centers in India, we analyzed the clinical course and genotype of 54 patients from 37 families. Family screening identified 19 new patients (35%) from 12 index cases. Then, 33 GLA gene variants were identified in 49/54 (90.7%) which included 11 novel and 22 known pathogenic variants. Of the 54 patients in our cohort, 40 patients had “classical” and 10 patients had a “nonclassical” presentation. The symptoms and signs included kidney dysfunction in 38/54 (70.3%), neuropathic pain in 34/54 (62.9%), left ventricular hypertrophy in 22/49 (44.8%) and stroke in 5/54 (9.2%). Female heterozygotes were 10/54 (18.5%) of whom 2 were index cases. There was a significant delay in reaching the diagnosis of 11.7 years. Enzyme replacement therapy was initiated in 28/54 (51.8%) patients with significant improvement of neuropathic pain and gastrointestinal symptoms. This study highlights the clinical presentation and mutational spectrum of FD in India and suggests that family screening and screening of high‐risk groups (hypertrophic cardiomyopathy, idiopathic chronic renal failure and cryptogenic stroke) could be the most cost‐effective strategies for early identification of FD.

Spine radiograph is an essential component of a skeletal survey. It provides important diagnostic clues to various types of skeletal dysplasia. In some conditions, a spine radiograph alone may be diagnostic and characteristic; but mostly, it yields more value as a part of the complete skeletal survey. In this article we will discuss about a few common lethal and non-lethal skeletal dysplasias and their characteristic imaging findings; primarily focusing on the spine radiograph.

Abstract Background Mutations in TSC1 or TSC2 gene cause tuberous sclerosis complex (TSC), an autosomal dominant disorder characterized by the formation of non-malignant hamartomas in multiple vital organs. TSC1 and TSC2 gene products form TSC heterodimer that senses specific cell growth conditions to control mTORC1 signalling. Methods In the present study 98 TSC patients were tested for variants in TSC1 and TSC2 genes and 14 novel missense variations were identified. The pathogenecity of these novel variations was determined by applying different bioinformatics tools involving computer aided protein modeling. Results Protein modelling could be done only for ten variants which were within the functional part of the protein. Homology modeling is the most reliable method for structure prediction of a protein. Since no sequence homology structure was available for the tuberin protein, three dimensional structure was modeled by a combination of homology modeling and the predictive fold recognition and threading method using Phyre2 threading server. The best template structures for model building of the TSC1 interacting domain, tuberin domain and GAP domain are the crystal structures of clathrin adaptor core protein, Rap1GAP catalytic domain and Ser/Thr kinase Tor protein respectively. Conclusions In this study, an attempt has been made to assess the impact of each novel missense variant based on their TSC1-TSC2 hydrophobic interactions and its effect on protein function.

Abstract Background Neuronal ceroid lipofuscinoses type I and type II (NCL1 and NCL2) also known as Batten disease are the commonly observed neurodegenerative lysosomal storage disorder caused by mutations in the PPT1 and TPP1 genes respectively. Till date, nearly 76 mutations in PPT1 and approximately 140 mutations, including large deletion/duplications, in TPP1 genes have been reported in the literature. The present study includes 34 unrelated Indian patients (12 females and 22 males) having epilepsy, visual impairment, cerebral atrophy, and cerebellar atrophy. Methods The biochemical investigation involved measuring the palmitoyl protein thioesterase 1 and tripeptidy peptidase l enzyme activity from the leukocytes. Based on the biochemical analysis all patients were screened for variations in either PPT1 gene or TPP1 gene using bidirectional Sanger sequencing. In cases where Sanger sequencing results was uninformative Multiplex Ligation-dependent Probe Amplification technique was employed. The online tools performed the protein homology modeling and orthologous conservation of the novel variants. Results Out of 34 patients analyzed, the biochemical assay confirmed 12 patients with NCL1 and 22 patients with NCL2. Molecular analysis of PPT1 gene in NCL1 patients revealed three known mutations (p.Val181Met, p.Asn110Ser, and p.Trp186Ter) and four novel variants (p.Glu178Asnfs*13, p.Pro238Leu, p.Cys45Arg, and p.Val236Gly). In the case of NCL2 patients, the TPP1 gene analysis identified seven known mutations and eight novel variants. Overall these 15 variants comprised seven missense variants (p.Met345Leu, p.Arg339Trp, p.Arg339Gln, p.Arg206Cys, p.Asn286Ser, p.Arg152Ser, p.Tyr459Ser), four frameshift variants (p.Ser62Argfs*19, p.Ser153Profs*19, p.Phe230Serfs*28, p.Ile484Aspfs*7), three nonsense variants (p.Phe516*, p.Arg208*, p.Tyr157*) and one intronic variant (g.2023_2024insT). No large deletion/duplication was identified in three NCL1 patients where Sanger sequencing study was normal. Conclusion The given study reports 34 patients with Batten disease. In addition, the study contributes four novel variants to the spectrum of PPT1 gene mutations and eight novel variants to the TPP1 gene mutation data. The novel pathogenic variant p.Pro238Leu occurred most commonly in the NCL1 cohort while the occurrence of a known pathogenic mutation p.Arg206Cys dominated in the NCL2 cohort. This study provides an insight into the molecular pathology of NCL1 and NCL2 disease for Indian origin patients.

Abstract Background 4H syndrome is a congenital hypomyelinating leukodystrophy characterized by hypodontia, hypomyelination and hypogonadotropic hypogonadism belonging to the Pol III-related leukodystrophies which arise due to mutations in the POLR3A or POLR3B gene. The clinical presentation is of neurodevelopmental delay or regression with ataxia, dystonia, nystagmus, delayed deciduous dentition and abnormal order of eruption of teeth. MRI brain shows a characteristic hypomyelination pattern. Several mutations have been described in the implicated genes but there are no reports on mutations seen in patients from India. Case presentation We report a 1½ year old girl, only child of a non-consanguinous couple who presented with delayed developmental milestones and delayed dentition. On physical examination she had downward slanting palpebral fissures, low set ears, smooth philtrum, hypodontia, prominent body hair and clitoromegaly. There was prominent horizontal nystagmus, hypertonia of both upper and lower limbs, exaggerated deep tendon jerks and flexor planter response. She had not attained complete head control and required support to sit. She showed absent waves on brainstem evoked response audiometry and her fundus examination showed bilateral optic atrophy with prolongation of P100 latencies on visual evoked potentials. MRI Brain showed hyperintensity of entire white matter with involvement of the internal and external capsule, frontal deep white matter and corpus callosum. Her karyotype was 46 XX and her endocrinal profile was unremarkable. Clinical exome sequencing identified an unreported mutation in the POLR3A gene. The same mutation was identified by Sanger sequencing in heterozygous state in both parents. The child is being managed with physiotherapy and developmental therapy. She has been provided with hearing aids and started on speech therapy. Parents were provided anticipatory guidance and genetic counselling about autosomal recessive nature of inheritance, risk of recurrence and need for follow-up. Conclusion 4H syndrome is a rare congenital hypomyelinating leukodystrophy inherited as an autosomal recessive disorder due to mutations in the POLR3A and POLR3B gene. Delay or regression of milestones, abnormalities in dentition and endocrinal perturbations are its hallmark. A novel mutation in the POLR3A gene resulting in amino acid substitution of arginine for glutamine at codon 808 (p.R808Q) was detected in exon 18 in our case.

The bony pelvis is constituted by the ilium, ischium, pubis, and sacrum. The pelvic radiograph is an important component of the skeletal survey performed in suspected skeletal dysplasia. Most of the common skeletal dysplasias have either minor or major radiological abnormalities; hence, knowledge of the normal radiological appearance of bony pelvis is vital for recognizing the early signs of various skeletal dysplasias. This article discusses many common and some uncommon radiological findings on pelvic radiographs along with the specific dysplasia in which they are seen; common differential diagnostic considerations are also discussed.

Purpose: Leber's hereditary optic neuropathy (LHON) is an inherited optic neuropathy characterized by subacute painless vision loss. The majority of LHON is caused due to one of the three primary mutations in the mitochondrial DNA (m.G3460A, m.G11778A, and m.T14484C). The frequency of these mutations differs in different populations. The purpose of this study is to observe the frequency of three common primary mutations in the North Indian population. Methods: Forty LHON patients within the age group of 10–50 years underwent molecular testing for primary mutations. For two patients, testing for mother and other siblings was also carried out, using bidirectional sequencing. Results: A total of 11 out of 40 (27.5%) patients were found to be carrying m.G11778A mutation. Siblings of two probands were also positive for the same mutation. In one family, two primary mutations (m.G11778A and m.T14484C) were found in the proband and in the mother as well. Conclusion: In this study, 27.5% mutation was detected in North Indian LHON families. These results suggest that m.G11778A mutation is more frequent in this population. The results of the present study are compatible with studies of an Asian population and Northern European population.

Objective: The objective of this study is to retrospectively collect and then describe the clinico-radiographical profile of confirmed cases of leukodystrophy who presented over a 5-year period to a tertiary care teaching hospital in North India. Materials and Methods: The case records of 80 confirmed cases of leukodystrophy were reviewed and the cases have been described in terms of their clinical presentation and neuroimaging findings. Results: The cases have been grouped into five categories: Hypomyelinating, demyelinating, disorders with vacuolization, cystic, and miscellaneous. The commonest leukodystrophies are megalencephalic leukoencephalopathy with subcortical cysts (MLC), Pelizaeus-Merzbacher disease (PMD), and metachromatic leukodystrophy (MLD). A notable proportion of hypomyelinating disorders were uncharacterized. Conclusions: Leukodystrophies at this point of time have no definite cure. They have a progressively downhill clinical course. Early diagnosis is imperative for appropriate genetic counseling. A simplified approach to diagnose common leukodystrophies has also been provided. It is important to develop a registry, which can provide valuable epidemiological data to prioritize research in this field, which has many unanswered questions.

Context: Treatment of patients with cleft lip and palate (CLP) anomaly requires a multidisciplinary approach from birth until adulthood. Many children with cleft anomaly are born in rural areas where resources for treatment and awareness on cleft care are limited. Consequently, many patients may receive limited or suboptimal care due to multitudes of reasons. Aims: The current study was aimed to record the baseline data on the spectrum of clinical profile of cleft patients, treatment protocols, quality of treatment and the residual treatment needs of patients with CLP anomaly visiting three major hospitals across Delhi and National Capital Region (NCR). The experience gained from the three-center study would be used to lay a framework to conduct a nationwide multicenter study in terms of logistics, feasibility and difficulties. Materials and Methods: The study titled "CLP anomaly in India: Clinical profile Risk factors and current status of treatment: A hospital based study" was started in 2010 as a Task Force project of Indian Council of Medical Research. The Pilot phase, which started in 2012, encompassed three cleft centers across Delhi and NCR, namely, All India Institute of Medical Sciences, Safdarjang Hospital and Medanta - The Medicity. Data for 126 non-syndromic CLP subjects was recorded on a specially designed performa. Each case was evaluated by a team of specialists comprising of a Plastic Surgeon, an Orthodontist, ENT Surgeon, Dental Surgeon, Speech therapist and an Audiologist. Clinical records included profile and intraoral photos, dental study models, audiometric and speech evaluation data. The current paper attempts to highlights a few of relevant observations of the pooled data from three centers. Results and Conclusions: The results indicate a lack of uniform protocol followed in providing care to cleft patients. A great variation was found in the quality of treatment received by many of the patients.

Peters’ plus syndrome is a rare but clinically recognizable autosomal recessive ocular genetic syndrome. Diagnosis during the fetal life is challenging due to the presence of nonspecific findings such as ventriculomegaly in the growth-retarded fetuses. We report the first case of fetal Peters’ plus syndrome from India, where fetal ultrasound and the family history were helpful in providing a clue to the diagnosis that was confirmed later on by the DNA analysis.