MedGenome Labs Ltd. – Publications | MedGenome - Part 4


At MedGenome, we are deeply focused on continuous innovation, and publishing our findings for the larger benefit of the genetic testing community. Read through our publications for details of our latest work.

Date: January 13, 2022

Autosomal aneuploidies occurring in chromosomes other than 13, 18, and 21 and sex chromosomal aneuploidies are referred to as ‘Rare autosomal aneuploidies’ (RAAs).
A prenatal incidence of 0.41% is noted for RAAs on chorionic villus sampling (CVS) procedures. Aneuploidies in autosomes other than 13, 18, and 21 and sex chromosomal aneuploidies may result in increased fetal-placental diseases
such as non-viable pregnancy, early miscarriage, intrauterine fetal growth restriction, uniparental disomy, multiple congenital anomalies, fetal demise, or normal live birth [1]. The screen-positive rate of RAAs on NIPT is 0.04% to 0.83%.
However, the PPV of RAAs on NIPT is found to be 6–29%.
The increased false positives for RAAs on NIPT are most commonly due to confined placental mosaicism (CPM) [2] but may also arise due to vanishing twin or maternal malignancies.
Clinically relevant abnormalities can be detected in 30–75% of the high-risk cases of RAAs in NIPT [1].

Date: January 13, 2022

References 1. Hsieh L, Nugent D (2008) Factor XIII deficiency. Haemophilia 14:1190–1200 2. Loewy AG, McDonagh J, Mikkola H, Teller DC, Yee VC (2001) Structure and function of factor XIII. In: Colmam RW, Hirsh J, Marder VJ, Clowes AW, George JN (eds) Hemostatis and thrombosis: basic principles and practice. Lippincott Williams and Wilkins, Philadelphia, pp 233–247

Date: February 9, 2023

Ocular dyskinesia (OD) is an uncommon form of the levodopa induced dyskinesia (LIOD) characterized by short-lasting horizontal or upward conjugate gaze deviation. More sustained deviations resembling oculogyric crises (OGC) are distinctly uncommon.1-4 A 62-yr-old man with a 10-yr history of Parkinson’s disease (PD) presented florid ocular dyskinesia mimicking OGC. Levodopa introduction caused increased blinking, up rolling of the eyeballs and dose-dependent restlessness lasting 48 hr with a single dose of 300 mg. Amantadine, safinamide, clonazepam, and dopamine agonists were without benefit, and he stayed off medication for 3 yr. The symptoms recurred after restarting levodopa at age 61. There was no relevant tic, dopamine blocker, encephalitis, or family history. His OFF-UPDRS-III score was 78 (Video 1). Within 10–15 min of levodopa 100 mg increased eyeblink, blepharospasm, right-sided horizontal/upward conjugate eye movements, buccolingual and peribuccal dyskinesia were noted (Video 2). Apomorphine (4 mg) resulted in similar ocular features. MRI brain was normal. Whole-exome sequencing showed variants of unknown significance in GBA p.Arg170His (also in his asymptomatic older sister) and LRRK2 p.Arg1943Trp genes.

Date: January 6, 2022

Background Inherited tubulopathies are a heterogeneous group of genetic disorders making whole-exome sequencing (WES) the preferred diagnostic methodology. Methods This was a multicenter descriptive study wherein children (< 18 years) with clinically suspected tubular disorders were recruited for molecular testing through WES. Multiplex ligation-dependent probe amplification (MLPA) and Sanger sequencing were done when required. Variants were classified as per American College of Medical Genetics 2015 guidelines and pathogenic (P)/likely pathogenic (LP) variants were considered causative. Results There were 77 index cases (male =73%). Median age at diagnosis was 48 months (IQR 18.5 to 108 months). At recruitment, the number of children in each clinical group was as follows: distal renal tubular acidosis (dRTA) = 25; Bartter syndrome = 18; isolated hypophosphatemic rickets (HP) = 6; proximal tubular dysfunction (pTD) = 12; nephrogenic diabetes insipidus (NDI) = 6; kidney stone/nephrocalcinosis (NC) = 6; others = 4. We detected 55 (24 novel) P/LP variants, providing genetic diagnoses in 54 children (70%). The diagnostic yield of WES was highest for NDI (100%), followed by HP (83%; all X-linked HP), Bartter syndrome (78%), pTD (75%), dRTA (64%), and NC (33%). Molecular testing had a definite impact on clinical management in 24 (31%) children. This included revising clinical diagnosis among 14 children (26% of those with a confirmed genetic diagnosis and 18% of the overall cohort), detection of previously unrecognized co-morbidities among 8 children (sensorineural deafness n = 5, hemolytic anemia n = 2, and dental changes n = 1) and facilitating specific medical treatment for 7 children (primary hyperoxaluria n = 1, cystinosis n = 4, tyrosinemia n = 2).

Date: January 6, 2022

Abstract Objective: To determine the demographic pattern of juvenile-onset parkinsonism (JP, <20 years), young-onset (YOPD, 20-40 years), and early onset (EOPD, 40-50 years) Parkinson’s disease (PD) in India. Materials and methods: We conducted a 2-year, pan-India, multicenter collaborative study to analyze clinical patterns of JP, YOPD, and EOPD. All patients under follow-up of movement disorders specialists and meeting United Kingdom (UK) Brain Bank criteria for PD were included. Results: A total of 668 subjects (M:F 455:213) were recruited with a mean age at onset of 38.7 ± 8.1 years. The mean duration of symptoms at the time of study was 8 ± 6 years. Fifteen percent had a family history of PD and 13% had consanguinity. JP had the highest consanguinity rate (53%). YOPD and JP cases had a higher prevalence of consanguinity, dystonia, and gait and balance issues compared to those with EOPD. In relation to nonmotor symptoms, panic attacks and depression were more common in YOPD and sleep-related issues more common in EOPD subjects. Overall, dyskinesias were documented in 32.8%. YOPD subjects had a higher frequency of dyskinesia than EOPD subjects (39.9% vs. 25.5%), but they were first noted later in the disease course (5.7 vs. 4.4 years).

Date: August 22, 2023

Abstract Background: India accounts for 20% of the global retinoblastoma (RB) burden. However, the existing data on RB1 gene germline mutations and its influence on clinical decisions is minimally explored. Methods: Fifty children with RB underwent complete clinical examination and appropriate multidisciplinary management. Screening of germline RB1 gene mutations was performed through next-generation sequencing and Multiplex Ligation-dependent Probe Amplification (MLPA) analysis. The mutation and non-mutation groups were compared for clinical parameters especially severity, progression and recurrence. Results: Twenty-nine patients had bilateral RB (BLRB) and 21 had unilateral RB (ULRB). The genetic analysis revealed 20 RB1 variations in 29 probands, inclusive of 3 novel mutations, known 16 mutations and heterozygous whole gene deletions. The mutation detection rate (MDR) was 86.2% in BLRB and 19% in ULRB. Associations of disease recurrence (p = 0.021), progression (p = 0.000) and higher percentage of optic nerve invasion, subretinal seeds and high-risk pathological factors were observed in the mutation group. Clinical management was influenced by the presence of germline mutations, particularly while deciding on enucleation, frequency of periodic follow up and radiotherapy.

Date: November 24, 2021

Excessive prenatal opioid exposure may lead to the development of Neonatal Opioid Withdrawal Syndrome (NOWS). RNA-seq was done on 64 formalin-fixed paraffin-embedded placental tissue samples from 32 mothers with opioid use disorder, with newborns with NOWS that required treatment, and 32 prenatally unexposed controls. We identified 93 differentially expressed genes in the placentas of infants with NOWS compared to unexposed controls. There were 4 up- and 89 downregulated genes. Among these, 7 genes CYP1A1, APOB, RPH3A, NRXN1, LINC01206, AL157396.1, UNC80 achieved an FDR p-value of <0.01. The remaining 87 genes were significant with FDR p-value <0.05. The 4 upregulated, CYP1A1, FP671120.3, RAD1, RN7SL856P, and the 10 most significantly downregulated genes were RNA5SP364, GRIN2A, UNC5D, DMBT1P1, MIR3976HG, LINC02199, LINC02822, PANTR1, AC012178.1, CTNNA2. Ingenuity Pathway Analysis identified the 7 most likely to play an important role in the etiology of NOWS. Our study expands insights into the genetic mechanisms of NOWS development.

Date: November 17, 2021

The THOC2 gene encodes THO complex subunit 2, a subunit of the Transcription-Export (TREX) complex which binds specifically to splice messenger ribonucleic acid (mRNAs) to facilitate mRNA export. Mutations in the THOC2 gene have been described to lead to X-linked mental retardation syndrome type 12/35 (XLMR-12/35) (MIM#300957). Here, we describe for the first time a recurrent arthrogryposis multiplex congenita phenotype (AMC) in two male fetuses in a family. Exome sequencing identified a novel pathogenic variation chrX: 122761817_122761820delTGAC (genome assembly GRCh37 format) or c.2482-1_2484delGTCA (as per Genbank transcript ID NM_001081550) in theTHOC2 gene. This variant affects the consensus acceptor splice site between intron 22 and exon 23. This is the most severe phenotype described in THOC2 gene-related disease till date. This case report expands the clinical phenotype of THOC2 gene related defects.

Date: November 9, 2021


Background: Sporadic nonlesional intractable visual-sensitive epilepsies of childhood represent a challenging subset of epilepsies in terms of management and prognostication given a propensity to evolve as epileptic encephalopathy.
Objective: To study the genetic heterogeneity of drug-resistant visual sensitive epilepsy of childhood.
Methods: A retrospective chart review was conducted on patients in the pediatric age group between 2016 and 2018, with drug-resistant epilepsy (DRE) and video electro encephalography (VEEG) documented reflex photosensitivity, eye-condition sensitivity. Those patients who underwent genetic testing with targeted next-generation sequencing using an epilepsy gene panel were selected.
Results: During the study period, out of 96 patients who underwent genetic testing, 4 patients (4.17%) with sporadic DRE presented with clinical phenotypes ranging from myoclonic-atonic epilepsy, generalized epilepsy with eyelid myoclonia as well as febrile and unprovoked seizures, along with visual sensitivity. Video EEG documented abnormalities ranged from occipital, posterior-cortex and generalized discharges with “eyes-closed state” triggered, self-induced “smart-phone” triggered, photosensitive focal-onset and generalized myoclonic seizures. Accompanying developmental impairment was noted. These patients who were investigated with clinical exome sequencing were detected to have mutations in not only SCN1A genes (pathogenic exonic and intronic variants) but also CHD2 (pathogenic) and CACNA1H genes (a familial febrile-seizure susceptibility variant of unknown significance).
Conclusions: The series highlights the complex genetics of drug-resistant visual-sensitive epilepsy of childhood. Such genotype–phenotype associations throw light on the role of ion-channel and non-ion channel genes on reflex epileptogenesis in this group of patients.

Date: October 2, 2021

ABSTRACT Background. The burden of hereditary breast cancer in India is not well defined. Moreover, genetic testing criteria (National Comprehensive Cancer Network [NCCN] and Mainstreaming Cancer Genetics [MCG] Plus) have never been validated in the Indian population. Methods. All new female breast cancer patients from 1st March 2019 to 28th February 2020 were screened. Those providing informed consent and without previous genetic testing were recruited. Multigene panel testing (107 genes) by next-generation sequencing was performed for all patients. The frequency of pathogenic/likely pathogenic (P/ LP) mutations between patients qualifying and not qualifying the testing criteria was compared and their sensitivity was computed. Results. Overall, 275 breast cancer patients were screened and 236 patients were included (median age 45 years); 30 patients did not consent and 9 patients previously underwent genetic testing. Thirty-four (14%) women had a positive family history and 35% had triple-negative breast cancer. P/LP mutations were found in 44/236 (18.64%).

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