A systematic review of inherited retinal dystrophies in Pakistan: updates from 1999 to April 2023

BACKGROUND

Inherited retinal degenerations (IRDs) are a group of rare genetic conditions affecting retina of the eye that range in prevalence from 1 in 2000 to 1 in 4000 people globally. This review is based on a retrospective analysis of research articles reporting IRDs associated genetic findings in Pakistani families between 1999 and April 2023.

METHODS

Articles were retrieved through survey of online sources, notably, PubMed, Google Scholar, and Web of Science. Following a stringent selection criterion, a total of 126 research articles and conference abstracts were considered. All reported variants were cross-checked and validated for their correct genomic nomenclature using different online resources/databases, and their pathogenicity scores were explained as per ACMG guidelines.

RESULTS

A total of 277 unique sequence variants in 87 distinct genes, previously known to cause IRDs, were uncovered. In around 70% cases, parents of the index patient were consanguineously married, and approximately 88.81% of the detected variants were found in a homozygous state. Overall, more than 95% of the IRDs cases were recessively inherited. Missense variants were predominant (41.88%), followed by Indels/frameshift (26.35%), nonsense (19.13%), splice site (12.27%) and synonymous change (0.36%). Non-syndromic IRDs were significantly higher than syndromic IRDs (77.32% vs. 22.68%). Retinitis pigmentosa (RP) was the most frequently observed IRD followed by Leber's congenital amaurosis (LCA). Altogether, mutations in PDE6A gene was the leading cause of IRDs in Pakistani families followed by mutations in TULP1 gene.

CONCLUSION

In summary, Pakistani families are notable in expressing recessively inherited monogenic disorders including IRDs likely due to the highest prevalence of consanguinity in the country that leads to expression of rare pathogenic variants in homozygous state.

Development of preimplantation genetic testing for monogenic reference materials using next-generation sequencing

OBJECTIVE

Preimplantation genetic testing for monogenic disorders (PGT-M) has been used for over 20 years to detect many serious genetic conditions. However, there is still a lack of reference materials (RMs) to validate the test performance during the development and quality control of PGT-M.

METHOD

Sixteen thalassemia cell lines from four thalassemia families were selected to establish the RMs. Each family consisted of parents with heterozygous mutations for α- and/or β-thalassemia and two children, at least one of whom carried a homozygous thalassemia mutation (proband). The RM panel consisted of 12 DNA samples (parents and probands in 4 families) and 4 simulated embryos (cell lines constructed from blood samples from the four nonproband children). Four accredited genetics laboratories that offer verification of thalassemia samples were invited to evaluate the performance of the RM panel. Furthermore, the stability of the RMs was determined by testing after freeze‒thaw cycles and long-term storage.

RESULTS

PGT-M reference materials containing 12 genome DNA (gDNA) reference materials and 4 simulated embryo reference materials for thalassemia testing were successfully established. Next-generation sequencing was performed on the samples. The genotypes and haplotypes of all 16 PGT-M reference materials were concordant across the four labs, which used various testing workflows. These well-characterized PGT-M reference materials retained their stability even after 3 years of storage.

CONCLUSION

The establishment of PGT-M reference materials for thalassemia will help with the standardization and accuracy of PGT-M in clinical use.

OneGene PGT: comprehensive preimplantation genetic testing method utilizing next-generation sequencing

PURPOSE

Preimplantation genetic testing for monogenic disorders (PGT-M) allows early diagnosis in embryos conceived in vitro. PGT-M helps to prevent known genetic disorders in affected families and ensures that pathogenic variants in the male or female partner are not passed on to offspring. The trend in genetic testing of embryos is to provide a comprehensive platform that enables robust and reliable testing for the causal pathogenic variant(s), as well as chromosomal abnormalities that commonly occur in embryos. In this study, we describe PGT protocol that allows direct mutation testing, haplotyping, and aneuploidy screening.

METHODS

Described PGT protocol called OneGene PGT allows direct mutation testing, haplotyping, and aneuploidy screening using next-generation sequencing (NGS). Whole genome amplification product is combined with multiplex PCR used for SNP enrichment. Dedicated bioinformatic tool enables mapping, genotype calling, and haplotyping of informative SNP markers. A commercial software was used for aneuploidy calling.

RESULTS

OneGenePGT has been implemented for seven of the most common monogenic disorders, representing approximately 30% of all PGT-M indications at our IVF centre. The technique has been thoroughly validated, focusing on direct pathogenic variant testing, haplotype identification, and chromosome abnormality detection. Validation results show full concordance with Sanger sequencing and karyomapping, which were used as reference methods.

CONCLUSION

OneGene PGT is a comprehensive, robust, and cost-effective method that can be established for any gene of interest. The technique is particularly suitable for common monogenic diseases, which can be performed based on a universal laboratory protocol without the need for set-up or pre-testing.

Prenatal Genetic Diagnosis of Fetal Cystic Hygroma: A Retrospective Single-Center Study from China

Fetal cystic hygroma (CH) is associated with poor prognosis and chromosomal anomalies. Recent studies have suggested that the genetic background of affected fetuses is essential for predicting pregnancy outcomes. However, the detection performance of different genetic approaches for the etiological diagnosis of fetal CH remains unclear. In this study, we aimed to compare the diagnostic efficiency of karyotyping and chromosomal microarray analysis (CMA) in a local fetal CH cohort, and tried to propose an optimized testing strategy that may help improve the cost-effectiveness of disease management. We reviewed all pregnancies that underwent invasive prenatal diagnosis between January 2017 and September 2021 at one of the largest prenatal diagnostic centers in Southeast China. We collected cases identified by the presence of fetal CH. Prenatal phenotypes and laboratory records of these patients were audited, collated, and analyzed. The detection rates of karyotyping and CMA were compared, and the concordance rate of these two methods was calculated. A total of 157 fetal CH cases were screened from 6,059 patients who underwent prenatal diagnosis. Diagnostic genetic variants were identified in 44.6% (70/157) of the cases. Karyotyping, CMA, and whole-exome sequencing (WES) identified pathogenic genetic variants in 63, 68, and 1 case, respectively. The Cohen's κ coefficient between karyotyping and CMA was 0.96, with a concordance of 98.0%. Of the 18 cases in which cryptic copy number variants <5 Mb were detected by CMA, 17 were interpreted as variants of uncertain significance, and the remaining cases were interpreted as pathogenic. Trio exome sequencing revealed a pathogenic homozygous splice site mutation in the PIGN gene in a case undiagnosed by CMA and karyotyping. Our study demonstrated that chromosomal aneuploidy abnormalities are the main genetic cause of fetal CH. Based on this, we recommend karyotyping combined with rapid aneuploidy detection as a first-tier approach for the genetic diagnosis of fetal CH. WES and CMA could improve the diagnostic yield when routine genetic tests fail to determine the cause of fetal CH.

The neglected role of preimplantation genetic testing for Lynch syndrome

Preimplantation genetic testing for monogenic/single-gene disorders (PGT-M) is a procedure employed in the field of assisted reproductive technology to avoid the transmission of genetic diseases to the offspring. Hereditary cancer syndromes represent a diffuse and accepted indication for PGT-M, but take-up differs among the different disorders. Its use is markedly lower for the genes causing Lynch syndrome compared with the breast cancer type 1 or 2 susceptibility genes (BRCA1/2), despite the similar prevalence and severity of the two conditions. Reasons to explain this difference have not been explored. First, Lynch syndrome may be more frequently undiagnosed compared with hereditary breast and ovarian cancer syndrome. In addition, the different take-up may be due to different patient perceptions of the conditions and of the management options. Finally, this distinct attitude may depend on the awareness and sensibility of the professionals caring for affected patients. The authors' considerations are, however, speculative, and specific studies aimed at disentangling the causes of the different receptions of PGT-M are warranted to understand how to tackle this gap. In the meantime, we believe that empowerment regarding PGT-M of all individuals with hereditary cancer syndromes, including Lynch syndrome, is ethically due, and plead for a more active involvement of caregivers.

Amplicon sequencing-based carrier screening for 170 monogenic disorders among children with abnormal LC-MS/MS results

BACKGROUND

Next-generation sequencing (NGS) has been suggested as a second-tier diagnostic test for newborn screening, which could help identify the carrier status of hundreds monogenic disorders with wider spectrum and earlier stage.

METHODS

Among the 1087 children (age from 27 min to 14 years old) underwent liquid chromatography-tandem mass spectrometry (LC-MS/MS), 290 individuals who had at least one abnormal value of LC-MS/MS measurements were sent for amplicon sequencing-based carrier screening (targeting 141 genes for 170 monogenic disorders). Multiplex polymerase chain reaction was used for amplicon capture and library preparation, the NextSeq 500 NGS platform (Illumina PE150) was used for sequencing. The identified clinical significant variants were further validated by Sanger sequencing.

RESULTS

Only 89 children carry none of clinical significant variants, other 201 individuals carry 1-4 variants in 63 genes (132 types; 317 in total: 171 pathogenic, 37 likely pathogenic, 29 variants of unknown significance, and 80 disease-associated functional polymorphisms). Besides the three missing samples with 4 variants, 91.1 % of identified variants (285 variants in 54 genes) were completely validated by Sanger sequencing. The most common genetic variants were in UGT1A1, GJB2, PAH, G6PD, and SLC25A13 (top 5 genes), which corresponding to Gilbert/Crigler-Najjar symdrome (n = 89), autosomal recessive hearing loss type 1A (n = 58), phenylketonuria (n = 12), glucose-6-phosphate dehydrogenease deficiency (n = 11) and Citrin deficiency (n = 9). More than 42 children present higher phenylalanine in LC-MS/MS, but only 12 of them were identified to carry clinical significant variants in PAH gene.

CONCLUSION

The amplicon sequencing-based carrier screening in our study could further clarify the abnormal LC-MS/MS results, which could also discover more monogenic disorders uncovered by LC-MS/MS screening.

Combining PGT-A with PGT-M risks trying to do too much

The primary objective of preimplantation genetic testing for monogenic disorders (PGT-M) is to avoid having a child with a serious monogenic disease. Combining testing for unrelated sporadic chromosomal abnormalities (PGT-A) and excluding embryos with chromosomally abnormal results from transfer proffers the chance to mitigate the risk of miscarriage and to reduce the number of embryo transfers, but also risks excluding healthy embryos from transfer due to abnormal test results that do not reflect the true potential of the embryo. The theoretical utility of combining PGT-M with PGT-A is explored in this communication. It is concluded that PGT-M without PGT-A is preferred to achieve an unaffected live birth. Since PGT-M is mostly undertaken by couples where the female partner is younger than 35 years, PGT-A is likely to marginally mitigate the risk of miscarriage. Experimental non-selection studies are needed to assess the potential detrimental effect of combining PGT-M with PGT-A in a clinical setting.

Carrier screening and PGT for an autosomal recessive monogenic disorder: insights from virtual trials

PURPOSE

To assess the costs and benefits of carrier screening and preimplantation genetic testing (PGT) for recessive autosomal monogenic disorders for couples attempting assisted conception.

METHODS

A simulated first full cycle for women less than 35 years transferring embryos one at a time. The effect of testing on pregnancy outcomes was evaluated for different reporting scenarios. A Monte Carlo method utilising 1000 trials for 10,000 couples, testing 4, 16 and 38 genes, was used to assess the numbers likely to be at high risk and to estimate the incremental cost of screening and PGT to avoid an affected child.

RESULTS

PGT for high-risk couples: testing embryos only for the monogenic condition avoided 1 affected pregnancy for 4 cycles started. Combined with testing for chromosomal aneuploidy: ranking test results avoided 1 adverse pregnancy (affected, biochemical, clinical miscarriage) from 3 cycles started; 1 in 2 when excluding from transfer all embryos with an abnormal test result, within 1 in 25 fewer women achieving an unaffected live birth. Carrier screening for 4, 16 and 38 gene scenarios, where 1:250, 1:196 and 1:29 couples were at high risk: the incremental cost to prevent 1 affected live birth was estimated to be less than GBP 1,150,000 (US $1,587,000), < 836,642 (1,154,566) and < 137,794 (190,156), respectively, in 95% of trials.

CONCLUSIONS

Carrier screening combined with PGT, with and without testing for unrelated chromosomal abnormalities, for couples attempting assisted conception is complex but likely to be effective and also expensive.

A novel mutation of PCSK1 responsible for PC1/3 deficiency in two siblings

Proprotein convertase 1 (PCSK1, PC1/3) deficiency is an uncommon cause of neonatal malabsorptive diarrhoea associated with endocrinopathies that are due to the disrupted processing of a large number of prohormones, including proinsulin. To date, only 26 cases have been reported. Herein, we describe two siblings with typical features including severe congenital diarrhoea, central diabetes insipidus, growth hormone deficiency, and hypoadrenalism. Next generation sequencing found a homozygous missense mutation in exon 5 of PCSK1 gene, c.500A>C (p.Asp167Ala), located within the catalytic domain. Both patients presented a high level of proinsulin. In the first years of life they required parenteral nutrition and hormone replacement therapy. The patients, aged 3 and 1.5 years, experienced several infectious episodes associated with septic shocks. While the mechanism underlying intestinal failure remains poorly investigated, parenteral nutrition is essential in order to ensure normal growth in early childhood.

Newborn screening with targeted sequencing: a multicenter investigation and a pilot clinical study in China

Different newborn screening (NBS) programs have been practiced in many countries since the 1960s. It is of considerable interest whether next-generation sequencing is applicable in NBS. We have developed a panel of 465 causative genes for 596 early-onset, relatively high incidence, and potentially actionable severe inherited diseases in our Newborn Screening with Targeted Sequencing (NESTS) program to screen 11,484 babies in 8 Women and Children's hospitals nationwide in China retrospectively. The positive rate from preliminary screening of NESTS was 7.85% (902/11,484). With 45.89% (414/902) follow-up of preliminary positive cases, the overall clinically confirmative diagnosis rate of monogenic disorders was 12.07% (50/414), estimating an average of 0.95% (7.85% × 12.07%) clinical diagnosis rate, suggesting that monogenic disorders account for a considerable proportion of birth defects. The disease/gene spectrum varied in different regions of China. NESTS was implemented in a hospital by screening 3923 newborns to evaluate its clinical application. The turn-around time of a primary report, including the sequencing period of < 7 days, was within 11 days by our automatic interpretation pipeline. Our results suggest that NESTS is feasible and cost-effective as a first-tier NBS program, which will change the status of current clinical practice of NBS in China.

Physician-directed genetic screening to evaluate personal risk for medically actionable disorders: a large multi-center cohort study

BACKGROUND

The use of proactive genetic screening for disease prevention and early detection is not yet widespread. Professional practice guidelines from the American College of Medical Genetics and Genomics (ACMG) have encouraged reporting pathogenic variants that confer personal risk for actionable monogenic hereditary disorders, but only as secondary findings from exome or genome sequencing. The Centers for Disease Control and Prevention (CDC) recognizes the potential public health impact of three Tier 1 actionable disorders. Here, we report results of a large multi-center cohort study to determine the yield and potential value of screening healthy individuals for variants associated with a broad range of actionable monogenic disorders, outside the context of secondary findings.

METHODS

Eligible adults were offered a proactive genetic screening test by health care providers in a variety of clinical settings. The screening panel based on next-generation sequencing contained up to 147 genes associated with monogenic disorders within cancer, cardiovascular, and other important clinical areas. Sequence and intragenic copy number variants classified as pathogenic, likely pathogenic, pathogenic (low penetrance), or increased risk allele were considered clinically significant and reported. Results were analyzed by clinical area and severity/burden of disease using chi-square tests without Yates' correction.

RESULTS

Among 10,478 unrelated adults screened, 1619 (15.5%) had results indicating personal risk for an actionable monogenic disorder. In contrast, only 3.1 to 5.2% had clinically reportable variants in genes suggested by the ACMG version 2 secondary findings list to be examined during exome or genome sequencing, and 2% had reportable variants related to CDC Tier 1 conditions. Among patients, 649 (6.2%) were positive for a genotype associated with a disease of high severity/burden, including hereditary cancer syndromes, cardiovascular disorders, or malignant hyperthermia susceptibility.

CONCLUSIONS

This is one of the first real-world examples of specialists and primary care providers using genetic screening with a multi-gene panel to identify health risks in their patients. Nearly one in six individuals screened for variants associated with actionable monogenic disorders had clinically significant results. These findings provide a foundation for further studies to assess the role of genetic screening as part of regular medical care.

Monogenic Disorders (PGT-M)

What are the ethical perspectives of preimplantation genetic testing in patients using/considering PGT-A compared to those using/considering PGT-M? A 17-item questionnaire administered online was used to assess ethical perspectives in US patients who recently used/considered PGT-A (n=80) vs. those who used/considered PGT-M (n=72). Kruskal-Wallis, Chi-square, and Fisher exact tests were conducted with STATA. Most PGT-A and PGT-M users/considerers supported using PGT to screen for diseases fatal in childhood (86-89%) and those causing lifelong disabilities (76-79%) and opposed using PGT to screen for non-medical physical (80-87%) or intellectual traits (74-86%). Both groups agreed that PGT aids in parental decision-making, although some expressed concern over its potential to lead to unforeseen consequences for society and the PGT offspring. More PGT-M than PGT-A users/considerers opposed implanting genetically abnormal embryos when requested by parents (29% PGT-A vs. 56% PGT-M, p = 0.007). For embryo disposition, more PGT-A users/considerers favored freezing (95% PGTA vs. 82% PGT-M, p = 0.018) or donating genetically normal embryos to research (73% PGT-A vs. 57% PGT-M, p = 0.044), while more PGT-M users/considerers supported donating embryos with known genetic abnormalities to research (56% PGT-A vs. 81% PGT-M, p = 0.001). Regardless of the reason for using PGT, users generally agreed on the acceptable and unacceptable uses for it, as well as the potential societal impact. PGT-M users/considerers expressed more opposition than PGT-A users/considerers to implanting embryos with a genetic alteration when requested by the parents.

Genome-wide noninvasive prenatal diagnosis of monogenic disorders: Current and future trends

Noninvasive prenatal diagnosis (NIPD) is a risk-free alternative to invasive methods for prenatal diagnosis, e.g. amniocentesis. NIPD is based on the presence of fetal DNA within the mother’s plasma cell-free DNA (cfDNA). Though currently available for various monogenic diseases through detection of point mutations, NIPD is limited to detecting one mutation or up to several genes simultaneously. Noninvasive prenatal whole exome/genome sequencing (WES/WGS) has demonstrated genome-wide detection of fetal point mutations in a few studies. However, Genome-wide NIPD of monogenic disorders currently has several challenges and limitations, mainly due to the small amounts of cfDNA and fetal-derived fragments, and the deep coverage required. Several approaches have been suggested for addressing these hurdles, based on various technologies and algorithms. The first relevant software tool, Hoobari, recently became available. Here we review the approaches proposed and the paths required to make genome-wide monogenic NIPD widely available in the clinic.

Novel PGD strategy based on single sperm linkage analysis for carriers of single gene pathogenic variant and chromosome reciprocal translocation

PURPOSE

Preimplantation genetic diagnosis (PGD) analysis can be challenging for couples who carry more than one genetic condition. In this study, we describe a new PGD strategy to select which embryo(s) to transfer for two clinically challenging cases. Both cases lack essential family members for linkage analysis including de novo mutation combined with reciprocal translocation.

METHODS

Diverging from conventional method, we performed direct point mutation detection, quantitative analysis of gene copy number, combined with linkage analysis assisted by SNP information from single sperm (or polar bodies), thus establishing an all-in-one protocol for single embryonic cell preimplantation diagnosis for two co-existing genetic conditions (monogenic disease and chromosomal abnormality) on the NGS-based platform.

RESULTS

Using this newly developed method, 15 embryos from two cases were screened, and two embryos were determined as free of the monogenic disease and specific chromosomal abnormalities created by the prospective father's reciprocal translocations.

CONCLUSION

This novel PGD strategy could effectively select unaffected embryo(s) for couples affected with or carrying a monogenetic disease and a reciprocal chromosome translocation concurrently.

The most recurrent monogenic disorders that overlap with the phenotype of Rett syndrome

Rett syndrome (RTT) is an early-onset neurodevelopmental disorder that is caused by mutations in the MECP2 gene; however, defects in other genes (CDKL5 and FOXG1) can lead to presentations that resemble classic RTT, although they are not completely identical. Here, we attempted to identify other monogenic disorders that share features of RTT. A total of 437 patients with a clinical diagnosis of RTT-like were studied; in 242 patients, a custom panel with 17 genes related to an RTT-like phenotype was run via a HaloPlex-Target-Enrichment-System. In the remaining 195 patients, a commercial TruSight-One-Sequencing-Panel was analysed. A total of 40 patients with clinical features of RTT had variants which affect gene function in six genes associated with other monogenic disorders. Twelve patients had variants in STXBP1, nine in TCF4, six in SCN2A, five in KCNQ2, four in MEF2C and four in SYNGAP1. Genetic studies using next generation sequencing (NGS) allowed us to study a larger number of genes associated with RTT-like simultaneously, providing a genetic diagnosis for a wider group of patients. These new findings provide the clinician with more information and clues that could help in the prevention of future symptoms or in pharmacologic therapy.

Modeling blood diseases with human induced pluripotent stem cells

Induced pluripotent stem cells (iPSCs) are derived from somatic cells through a reprogramming process, which converts them to a pluripotent state, akin to that of embryonic stem cells. Over the past decade, iPSC models have found increasing applications in the study of human diseases, with blood disorders featuring prominently. Here, we discuss methodological aspects pertaining to iPSC generation, hematopoietic differentiation and gene editing, and provide an overview of uses of iPSCs in modeling the cell and gene therapy of inherited genetic blood disorders, as well as their more recent use as models of myeloid malignancies. We also discuss the strengths and limitations of iPSCs compared to model organisms and other cellular systems commonly used in hematology research.

Live birth rate is associated with oocyte yield and number of biopsied and suitable blastocysts to transfer in preimplantation genetic testing (PGT) cycles for monogenic disorders and chromosomal structural rearrangements

Objectives

To investigate whether live birth (LB) is associated with oocyte yield and number of biopsied and suitable blastocyst to transfer following preimplantation genetic testing (PGT) for monogenic disorders (PGT-M) and chromosomal structural rearrangements (PGT-SR).

Study design

All couples underwent controlled ovarian stimulation, blastocyst biopsy, vitrification and transfer of suitable embryo(s) in a frozen embryo transfer (FET) cycle.

Results

Of 175 couples who underwent PGT treatment, 249 oocytes retrievals were carried out and 230 FET were subsequently undertaken. 122/230 (53%, 95% CI 47-59) FET resulted in a LB and 16/230 (7%, 95% CI 4-11) have resulted in ongoing pregnancies. 21/230 (9%, 95% CI 6-14) FET resulted in miscarriage and 69/230 (30%, 95% CI 24-36) concluded with failed implantation. Two (1%, 95% CI 0-3) transfers underwent termination for congenital malformation, with no evidence of misdiagnosis by prenatal testing. The relationship between number of oocytes retrieved and number of blastocysts biopsied and suitable embryos to transfer were significant (p = 0.00; Incidence rate ratio (IRR) 1.05; 95% 1.04-1.06; p = 0.00; IRR 1.04; 95%, 1.03-1.06), respectively. The number of oocytes collected (p = 0.007; OR 1.06; 95% CI 1.01-1.10), the number of blastocysts biopsied (p = 0.001; OR 1.14; 95% 95% CI 1.06-1.23) and the number of suitable embryos to transfer (p = 0.00; OR 1.38; 95% CI 1.17-1.64) were all significantly associated with the odds of achieving a LB. There is a 14% and 38% increased chance of a LB per additional blastocyst biopsied and suitable embryo to transfer, respectively.

Conclusions

PGT-M and PGT-SR outcomes are significantly associated with egg yield, number of blastocysts to biopsy and suitable embryos to transfer.

Update on the use of exome sequencing in the diagnosis of fetal abnormalities

Unexpected fetal abnormalities detected through ultrasound scanning in pregnancy may have a monogenic aetiology but are difficult to diagnose. Next generation sequencing now enables us to sequence fetal exomes, providing increased resolution and broader diagnostic capability compared to traditional cytogenetic prenatal tests, improving the yield and accuracy of diagnoses and allowing better counselling for expectant parents. Here we review published studies of exome sequencing (ES) for prenatal diagnosis over the last 5 years and address important questions for its clinical implementation, including clinical utility, which groups benefit most, and practical and ethical challenges for interpreting and reporting results. We observe that fetal ES substantially improves diagnostic yield relative to cytogenetic techniques. However, diagnostic rates vary widely between studies, largely attributable to differences in case selection. Recently several large studies report variations in diagnostic yield between phenotypic groups, with fetuses with multisystem abnormalities most likely to receive a diagnosis from fetal ES. Challenges for prenatal ES include the limitations of ultrasound-based fetal phenotyping, the need for rapid return of results in pregnancy, and technical limitations compared to whole genome sequencing. We also consider ethical issues around potential secondary findings and variants of uncertain significance and the complex counselling needs these present. Prenatal ES is a valuable tool to diagnose fetal abnormalities and, as it is implemented in the clinic, more large-scale research will serve to further delineate its clinical utility, as well as generating new knowledge about fetal phenotypes and informing guidelines for case selection, reporting results and genetic counselling.

The role of clinical and neuroimaging features in the diagnosis of CADASIL

BACKGROUND

Cerebral autosomal dominant arteriopathy with subcortical infarcts and leukoencephalopathy (CADASIL) is the most common familial cerebral small vessel disease, caused by NOTCH3 gene mutations. The aim of our study was to identify clinical and neuroradiological features which would be useful in identifying which patients presenting with lacunar stroke and TIA are likely to have CADASIL.

METHODS

Patients with lacunar stroke or TIA were included in the present study. For each patient, demographic and clinical data were collected. MRI images were centrally analysed for the presence of lacunar infarcts, microbleeds, temporal lobe involvement, global atrophy and white matter hyperintensities.

RESULTS

128 patients (mean age 56.3 ± 12.4 years) were included. A NOTCH3 mutation was found in 12.5% of them. A family history of stroke, the presence of dementia and external capsule lesions on MRI were the only features significantly associated with the diagnosis of CADASIL. Although thalamic, temporal pole gliosis and severe white matter hyperintensities were less specific for CADASIL diagnosis, the combination of a number of these factors together with familial history for stroke result in a higher positive predictive value and specificity.

CONCLUSIONS

A careful familial history collection and neuroradiological assessment can identify patients in whom NOTCH3 genetic testing has a higher yield.

Beyond screening for chromosomal abnormalities: Advances in non-invasive diagnosis of single gene disorders and fetal exome sequencing

Emerging genomic technologies, largely based around next generation sequencing (NGS), are offering new promise for safer prenatal genetic diagnosis. These innovative approaches will improve screening for fetal aneuploidy, allow definitive non-invasive prenatal diagnosis (NIPD) of single gene disorders at an early gestational stage without the need for invasive testing, and improve our ability to detect monogenic disorders as the aetiology of fetal abnormalities. This presents clinicians and scientists with novel challenges as well as opportunities. In addition, the transformation of prenatal genetic testing arising from the introduction of whole genome, exome and targeted NGS produces unprecedented volumes of data requiring complex analysis and interpretation. Now translating these technologies to the clinic has become the goal of clinical genomics, transforming modern healthcare and personalized medicine. The achievement of this goal requires the most progressive technological tools for rapid high-throughput data generation at an affordable cost. Furthermore, as larger proportions of patients with genetic disease are identified we must be ready to offer appropriate genetic counselling to families and potential parents. In addition, the identification of novel treatment targets will continue to be explored, which is likely to introduce ethical considerations, particularly if genome editing techniques are included in these targeted treatments and transferred into mainstream personalized healthcare. Here we review the impact of NGS technology to analyse cell-free DNA (cfDNA) in maternal plasma to deliver NIPD for monogenic disorders and allow more comprehensive investigation of the abnormal fetus through the use of exome sequencing.

The Genetics of Food Allergy

PURPOSE OF REVIEW

Food allergy likely arises from a complex interplay between environmental triggers and genetic susceptibility. Here, we review recent studies that have investigated the genetic pathways and mechanisms that may contribute to the pathogenesis of food allergy.

RECENT FINDINGS

A heritability component of food allergy has been observed in multiple studies. A number of monogenic diseases characterized by food allergy have elucidated pathways that may be important in pathogenesis. Several population-based genetic variants associated with food allergy have also been identified. The genetic mechanisms that play a role in the development of food allergy are heterogeneous and complex. Advances in our understanding of the genetics of food allergy, and how this predisposition interacts with environmental exposures to lead to disease, will improve our understanding of the key pathways leading to food allergy and inform more effective prevention and treatment strategies.

Implementing Non-Invasive Prenatal Diagnosis (NIPD) in a National Health Service Laboratory; From Dominant to Recessive Disorders

Our UK National Health Service regional genetics laboratory offers NIPD for autosomal dominant and de novo conditions (achondroplasia, thanataphoric dysplasia, Apert syndrome), paternal mutation exclusion for cystic fibrosis and a range of bespoke tests. NIPD avoids the risks associated with invasive testing, making prenatal diagnosis more accessible to families at high genetic risk. However, the challenge remains in offering definitive diagnosis for autosomal recessive diseases, which is complicated by the predominance of the maternal mutant allele in the cell-free DNA sample and thus requires a variety of different approaches. Validation and diagnostic implementation for NIPD of congenital adrenal hyperplasia (CAH) is further complicated by presence of a pseudogene that requires a different approach. We have used an assay targeting approximately 6700 heterozygous SNPs around the CAH gene (CYP21A2) to construct the high-risk parental haplotypes and tested this approach in five cases, showing that inheritance of the parental alleles can be correctly identified using NIPD. We are evaluating various measures of the fetal fraction to help determine inheritance of parental mutations. We are currently exploring the utility of an NIPD multi-disorder panel for autosomal recessive disease, to make testing more widely applicable to families with a variety of serious genetic conditions.