The Israeli National Genetic database: a 10-year experience

Unbiased phenotype and genotype matching maximizes gene discovery and diagnostic yield

PURPOSE

Widespread application of next-generation sequencing, combined with data exchange platforms, has provided molecular diagnoses for countless families. To maximize diagnostic yield, we implemented an unbiased semi-automated genematching algorithm based on genotype and phenotype matching.

METHODS

Rare homozygous variants identified in 2 or more affected individuals, but not in healthy individuals, were extracted from our local database of ∼12,000 exomes. Phenotype similarity scores (PSS), based on human phenotype ontology terms, were assigned to each pair of individuals matched at the genotype level using HPOsim.

RESULTS

33,792 genotype-matched pairs were discovered, representing variants in 7567 unique genes. There was an enrichment of PSS ≥0.1 among pathogenic/likely pathogenic variant-level pairs (94.3% in pathogenic/likely pathogenic variant-level matches vs 34.75% in all matches). We highlighted founder or region-specific variants as an internal positive control and proceeded to identify candidate disease genes. Variant-level matches were particularly helpful in cases involving inframe indels and splice region variants beyond the canonical splice sites, which may otherwise have been disregarded, allowing for detection of candidate disease genes, such as KAT2A, RPAIN, and LAMP3.

CONCLUSION

Semi-automated genotype matching combined with PSS is a powerful tool to resolve variants of uncertain significance and to identify candidate disease genes.

Potential Founder Variants in COL4A4 Identified in Bukharian Jews Linked to Autosomal Dominant and Autosomal Recessive Alport Syndrome

BACKGROUND

Alport syndrome is a hereditary disorder caused by pathogenic variants in the COL4A gene, which can be inherited in an autosomal recessive, dominant, or X-linked pattern. In the Bukharian Jewish population, no founder pathogenic variant has been reported in COL4A4.

METHODS

The cohort included 38 patients from 22 Bukharian Jewish families with suspected Alport syndrome who were referred the nephrogenetics clinic between 2012 and 2022. The study collected demographic, clinical, and genetic data from electronic medical records, which were used to evaluate the molecular basis of the disease using Sanger sequencing, and next-generation sequencing.

RESULTS

Molecular diagnosis was confirmed in 20/38 patients, with each patient having at least one of the three disease-causing COL4A4 variants detected: c.338GA (p.Gly1008Arg), and c.871-6T>C. In addition, two patients were obligate carriers. Overall, there were 17 heterozygotes, 2 compound heterozygotes, and 3 homozygotes. Each variant was detected in more than one unrelated family. All patients had hematuria with/without proteinuria at referral, and the youngest patient with proteinuria (age 5 years) was homozygous for the c.338G>A variant. End-stage renal disease was diagnosed in two patients at the age of 38 years, a compound heterozygote for c.338G>A and c.871-6T>C. Hearing deterioration was detected in three patients, the youngest aged 40 years, all of whom were heterozygous for c.338G>A.

CONCLUSION

This study unveils three novel disease-causing variants, c.3022G>A, c.871-6T>C, and c.338G>A, in the COL4A4 gene that are recurrent among Jews of Bukharian ancestry, and cause Alport syndrome in both dominant and recessive autosomal inheritance patterns.

Ethnic Differences in Clinical Presentations and Esophageal High-Resolution Manometry Findings in Patients with Achalasia

BACKGROUND

Ethnic differences in achalasia presentations have scarcely been described. The association between achalasia and immunologic HLA haplotypes suggests that there may be a genetic predisposition. We aimed to evaluate differences in demographic, clinical, endoscopic, and manometric findings between two distinct ethnic groups with achalasia-Israeli Arabs (IA) and Israeli Jews (IJ).

METHODS

A retrospective study was performed at two medical centers. High-resolution manometry (HRM) reports were reviewed for newly-diagnosed achalasia patients. Demographic data, clinical presentations, endoscopy reports, and HRM metrics including the integrated relaxation pressure (IRP) were all reviewed.

RESULTS

Overall, 94 achalasia patients were included (53.2% male; mean age 54.5 ± 18.0). 43 patients were IA (45.7%). Body mass index (BMI) was similar in both groups. Compared to IJ, the IA patients had more esophageal dysphagia (100% vs. 88.2%; P = 0.022), chest pain (46.5% vs. 25.5%; P = 0.033), and a tortuous esophagus on endoscopy (23.3% vs. 3.9%; p = 0.005). IA patients were also diagnosed at a younger age than IJ patients (50.9 ± 17.5 vs. 57.5 ± 18.0; p = 0.039). Furthermore, IRP values were higher among IA patients than IJ patients (32.2 ± 13.8 vs. 23.3 ± 8.4; p < 0.001). A regression model analysis found that ethnicity significantly predicted IRP (β = - 10, p < .001).

CONCLUSION

Ethnicity appears to affect achalasia clinical presentation and HRM findings. IA achalasia patients are diagnosed at a younger age, present with more severe esophageal symptoms, and have a higher IRP compared to IJ patients. Additional studies of diverse, multiethnic populations, especially with genetic evaluations, are required to further assess the role of ethnicity in achalasia.

Expert opinion on diagnosing, treating and managing patients with cerebrotendinous xanthomatosis (CTX): a modified Delphi study

Background

Cerebrotendinous xanthomatosis (CTX) is a rare, chronic, progressive, neurodegenerative disorder requiring life-long care. Patients with CTX often experience a diagnostic delay. Although early diagnosis and treatment initiation can improve symptoms and prognosis, a standardised approach to diagnosis, treatment and management of patients is not yet established.

Aim

To assess expert opinion on best care practices for patients with CTX using a modified Delphi method.

Methods

A multidisciplinary group of healthcare professionals with expertise in CTX responded to a 3-round online questionnaire (n = 10 in Rounds 1 and 2; n = 9 in Round 3), containing questions relating to the diagnosis, treatment, monitoring, multidisciplinary care and prognosis of patients with CTX. Determination of consensus achievement was based on a pre-defined statistical threshold of ≥ 70% Delphi panellists selecting 1–2 (disagreement) or 5–6 (agreement) for 6-point Likert scale questions, or ≥ 70% Delphi panellists choosing the same option for ranking and proportion questions.

Results

Of the Round 1 (n = 22), Round 2 (n = 32) and Round 3 (n = 26) questions for which consensus was assessed, 59.1%, 21.9% and 3.8% reached consensus, respectively. Consensus agreement that genetic analyses and/or determination of serum cholestanol levels should be used to diagnose CTX, and dried bloodspot testing should facilitate detection in newborns, was reached. Age at diagnosis and early treatment initiation (at birth, where possible) were considered to have the biggest impact on treatment outcomes. All panellists agreed that chenodeoxycholic acid (CDCA) is a lifetime replacement therapy which, if initiated early, can considerably improve prognosis as it may be capable of reversing the pathophysiological process in CTX. No consensus was reached on the value of cholic acid therapy alone. Monitoring patients through testing plasma cholestanol levels and neurologic examination was recommended, although further research regarding monitoring treatment and progression of the disease is required. Neurologists and paediatricians/metabolic specialists were highlighted as key clinicians that should be included in the multidisciplinary team involved in patients’ care.

Conclusions

The results of this study provide a basis for standardisation of care and highlight key areas where further research is needed to inform best practices for the diagnosis, treatment and management of patients with CTX.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13023-021-01980-5.

Prediction of Childhood Obesity from Nationwide Health Records

OBJECTIVE

To evaluate body mass index (BMI) acceleration patterns in children and to develop a prediction model targeted to identify children at high risk for obesity before the critical time window in which the largest increase in BMI percentile occurs.

STUDY DESIGN

We analyzed electronic health records of children from Israel's largest healthcare provider from 2002 to 2018. Data included demographics, anthropometric measurements, medications, diagnoses, and laboratory tests of children and their families. Obesity was defined as BMI ≥95th percentile for age and sex. To identify the time window in which the largest annual increases in BMI z score occurs during early childhood, we first analyzed childhood BMI acceleration patterns among 417 915 adolescents. Next, we devised a model targeted to identify children at high risk before this time window, predicting obesity at 5-6 years of age based on data from the first 2 years of life of 132 262 children.

RESULTS

Retrospective BMI analysis revealed that among adolescents with obesity, the greatest acceleration in BMI z score occurred between 2 and 4 years of age. Our model, validated temporally and geographically, accurately predicted obesity at 5-6 years old (area under the receiver operating characteristic curve of 0.803). Discrimination results on subpopulations demonstrated its robustness across the pediatric population. The model's most influential predictors included anthropometric measurements of the child and family. Other impactful predictors included ancestry and pregnancy glucose.

CONCLUSIONS

Rapid rise in the prevalence of childhood obesity warrant the development of better prevention strategies. Our model may allow an accurate identification of children at high risk of obesity.

Barriers and Considerations for Diagnosing Rare Diseases in Indigenous Populations

Advances in omics and specifically genomic technologies are increasingly transforming rare disease diagnosis. However, the benefits of these advances are disproportionately experienced within and between populations, with Indigenous populations frequently experiencing diagnostic and therapeutic inequities. The International Rare Disease Research Consortium (IRDiRC) multi-stakeholder partnership has been advancing toward the vision of all people living with a rare disease receiving an accurate diagnosis, care, and available therapy within 1 year of coming to medical attention. In order to further progress toward this vision, IRDiRC has created a taskforce to explore the access barriers to diagnosis of rare genetic diseases faced by Indigenous peoples, with a view of developing recommendations to overcome them. Herein, we provide an overview of the state of play of current barriers and considerations identified by the taskforce, to further stimulate awareness of these issues and the passage toward solutions. We focus on analyzing barriers to accessing genetic services, participating in genomic research, and other aspects such as concerns about data sharing, the handling of biospecimens, and the importance of capacity building.

The decision-making process, experience, and perceptions of preimplantation genetic testing (PGT) users

PURPOSE

The decision to undergo preimplantation genetic testing (PGT) entails a variety of personal and societal variables. Although PGT technology is widely accepted and used, few studies have queried the motives and concerns of PGT users; moreover, in-depth qualitative data regarding the PGT experience is scant.

METHODS

In order to explore and analyze the experience, concerns, expectations, and attitudes toward the PGT technique and its implications, semi-structured interviews were conducted in a single tertiary medical center with 43 Israeli PGT users for HLA matching and autosomal dominant, autosomal recessive, and X-linked genetic disorders.

RESULTS

The primary considerations in choosing PGT were prevention of birth of a child who would suffer a terminal or chronic disease as well as abrogation of a familial genetic condition. Religion played a decisive role in accepting PGT as an antenatal option. Regarding satisfaction with the PGT experience, many interviewees highlighted the need for greater attention to be given to potential stages of failure throughout the procedure and the need for emotional support. Our clinical results regarding implantation rate and cumulative live birth rate are 38-40% and 27-30%, respectively.

CONCLUSION

This survey broadens understanding of the specialized needs of women, couples, and minority groups undergoing PGT and underscores the relevance of counseling services for PGT users.

Impact of a national genetic carrier-screening program for reproductive purposes

INTRODUCTION

The Israeli population, encompassing 9 million citizens, is comprised of diverse communities. The Ministry of Health genetic screening program for reproductive purposes was introduced in 2013. This program is mainly aimed at severe incurable diseases with high rates of infant and childhood morbidity and/or mortality, with a carrier frequency of at least 1:60 and/or a disease frequency of 1 in 15 000 live births. In this paper, we present the results of the national genetic carrier-screening program implementation.

MATERIAL AND METHODS

Data acquisition for this study was performed by retrospectively searching Ministry of Health database, which includes the reports of 18 genetic laboratories performing genetic screening tests.

RESULTS

During 2015-2017, a total of 919 820 carrier-screening genetic tests were executed. The overall number rose by 14.9% over these years. For about two-thirds of the presented disorders, carrier frequency was within the expected range. A decrease of 57% was noted in the observed number of patients with spinal muscular atrophy born during 2014-2017, compared with the expected rate. Familial dysautonomia, Canavan and Tay-Sachs diseases yielded a very low prevalence.

CONCLUSIONS

Our results highlight the impact of a national genetic carrier-screening program. Couples at risk of an affected fetus mostly choose to perform preconception or prenatal diagnosis and to act accordingly. Our country has several characteristics enabling us to achieve this success, including considerable rates of endogamy and consanguineous marriages, increased frequency of founder mutations, and high fertility rates. In addition, wide accessibility of the tests and good compliance of the population must be noted. Still, raising the awareness and continuing education of population and caregivers about the importance and efficiency of carrier screening remains an important issue. Finally, expanding the existing tests into a uniform, wide genetic panel seems to be the next goal.

Ashkenazi Jewish genomic variants: integrating data from the Israeli National Genetic Database and gnomAD

PURPOSE

The aim of the study was to compare the data for mutations related to clinical disorders reported among Ashkenazi Jewish patients in the Israeli National Genetic Database (INGD) with variants included in the Genome Aggregation Database (gnomAD).

METHODS

We extracted data for mutations claimed to cause disorders reported among Ashkenazi Jews from the INGD and searched gnomAD for each of them. We compared the allele frequency of each variant in Ashkenazi Jews with that of other delineated populations.

RESULTS

Of the 58 INGD-reported mutations related to autosomal-dominant disorders, 19 were present in gnomAD (32.8%). Of the 309 mutations related to autosomal-recessive disorders, 240 (77.7%) were variants found in gnomAD. Of these variants, 202 (84.2%) were documented among one or more Ashkenazi individuals. At this point in the INGD, there are 168 Ashkenazi assumed founder mutations in 128 different genes corresponding to 111 autosomal-recessive disorders.

CONCLUSION

Integration of information on mutations among Ashkenazi Jews extracted from the INGD with their population frequency recorded in gnomAD is important for effective straightforward molecular diagnosis as well as for targeted carrier screening either for reproductive decision-making or for implementation of disease-modifying behavior.