Advances in clinical genetics and its current challenges.

The great advances in the development of genomic technologies and their incorporation into routine clinical practice is bringing about a change in which an individual's genetic information is becoming increasingly relevant to their medical care. This is known as genomic medicine. Its implementation is not without barriers, including difficulties in the assessment and interpretation of genomic data, deficient training of professionals and patients in this field, unequal access to units with expertise, and a lack of professional profiles and infrastructures necessary for the incorporation of genomic technologies into routine clinical practice. This article reviews the advances and challenges of genomic medicine.

Genetic counseling, virtual visits, and equity in the era of COVID-19 and beyond.

Overnight, as a result of the COVID-19 pandemic, telehealth rapidly transitioned from limited application to widespread implementation. The field of genetic counseling was well positioned to make this transition to virtual care since there is generally less of a need for patients to be seen in-person for physical exams or urgent care. Going forward, virtual visits will presumably become a mainstay in the provision of genetic services and it is anticipated that clinics will adopt "hybrid" models with both in-person and virtual visit options. This commentary highlights the successes and challenges in the rapid implementation of virtual visits, focusing on who has benefited versus who has been challenged or left behind. We also discuss genetic testing considerations, including the additional steps required for patients and clinicians when testing is ordered outside of the clinical setting, which can result in delays or a lack of testing altogether. Future research considerations are presented to address the needs among the most vulnerable and help ensure equitable access and benefit.

Cap a la genètica assistencial interdisciplinària i transversal: evolució de cinquanta anys en un hospital terciari a partir de la pediatria / Hacia la genètica asistencial interdisciplinaria y transversal: evolución de cincuenta años en un hospital terciario a partir de la pediatría / Towards interdisciplinary and transversal clinical genetics: a 50-year evolution from pediatrics in a tertiary hospital

L’objectiu d’aquest treball és analitzar l’evolució de la demanda assistencial i les possibilitats diagnòstiques, en laconsulta de genètica clínica d’un hospital de tercer nivell durant els últims cinquanta anys i també a partir dels seus inicis com a consulta específica de Pediatria.S’hi analitzen tant els motius de consulta com les proves de laboratori disponibles per arribar al diagnòstic dels pacients valorats durant el període 1968-2018, a la consulta de Genètica Clínica i al Laboratori de Genètica. A partir de 200 consultes anuals, en els primers anys, arribem a l’actualitat, en què se’n fan al voltant de 8.000 (entre primeres, successives i interconsultes), distribuïdes en Genètica Clínica i Assessorament Genètic, fins a un total de més de 32.000 pacients visitats durant aquests cinquanta anys.Al Laboratori de Genètica, l’evolució abasta des de l’estudi del cariotip convencional fins a l’aplicació de les tecnologies genòmiques actuals, i s’hi fan més de 9.000 estudis anuals de pacients de l’Hospital. Amb la incorporació de noves tecnologies moleculars s’ha canviat el paradigma de l’estudi genètic i s’ha aconseguit un rendiment millor: s’han pogut incrementar els diagnòstics i també s’ha reduït el temps necessari per obtenir-los.A més de la transformació del genetista que col·labora en el seguiment multidisciplinari dels pacients, s’evidencia uncanvi i una diversificació del motiu de consulta i s’estableix el valor de la incorporació, a partir del 2010, de professionals especialitzats en assessorament genètic per donar resposta a aquesta demanda.Els canvis experimentats en els motius de consulta, els diagnòstics i les proves de laboratori fetes durant tots aquests anys reflecteixen la importància de la incorporació i la interacció, en una mateixa àrea o unitat assistencial, de professionals especialitzats en genètica clínica, assessorament genètic i laboratori de genètica integral (també ambbioinformàtics). (AU)

El objetivo de este trabajo es analizar la evolución de la demandaasistencial y las posibilidades diagnósticas en la consulta de genética clínica de un hospital de tercer nivel a lo largo de los últimos50 años a partir de sus inicios como una consulta específica dePediatría.Se analizan los motivos de consulta y las pruebas de laboratorio disponibles para llegar al diagnóstico de los pacientes valorados en el período 1968-2018 en la Consulta de Genética Clínica y el Laboratorio de Genética. A partir de 200 consultas anuales en los primeros años llegamos a la actualidad, en que se realizan alrededor de 8.000 visitas (primeras, sucesivas e interconsultas) distribuidas en Genética Clínica y Asesoramiento Genético (32.000pacientes visitados hasta la fecha).En el laboratorio de Genética la evolución abarca desde el estudio del cariotipo convencional hasta la aplicación de las tecnologías genómicas actuales realizando más de 9.000 estudios anuales de pacientes del Hospital. Además de la transformación del genetista clínico colaborando en el seguimiento multidisciplinar de los pacientes, se evidencia un cambio y diversificación del motivo de consulta y se establece el valor de la incorporación de profesionales especializados en asesoramiento genético (a partir de 2010) para dar respuesta a esta demanda. Con la incorporación de nuevas tecnologías moleculares se ha cambiado el paradigma del estudio genético con un incremento importante del rendimiento y mejoría en el tiempo en obtener resultados diagnósticos. Los cambios experimentados en los motivos de consulta, los diagnósticos y las pruebas de laboratorio realizadas a lo largo de estos años reflejan la importancia de la incorporación e interacción, en una misma área/unidad asistencial, de profesionales especializados en genética clínica, asesores genéticos y laboratorio de genética integral (incluyendo bioinformáticos). (AU)

The objective of this work is to analyze the evolution of the demand and the diagnostic capabilities in the clinical genetics service of a tertiary hospital over the last 50 years from its initiationas a specific pediatric consultation. The reasons for consultationare analyzed as well as the laboratory tests available to reach thediagnosis of the patients evaluated in the period 1968-2018 at the Clinical Genetics Service and the Genetics Laboratory. From 200 consultations/year in the first years, we have reachedaround 8,000 visits (first, follow-up, and internal consultations) distributed in Clinical Genetics and Genetic Counseling (32,000patients visited to date).The Genetics Laboratory evolved from the study of the conventional karyotype to the application of state of the art genomic technologies, carrying out more than 9,000 annual studies from patients followed–up in the hospital.In addition to the transformation of the role of the clinical geneticist into a member of the multidisciplinary care team, there isevidence of a change and diversification of the reasons for consultation and in the value of incorporating professionals specializedin genetic counseling (starting in 2010) to respond to this demand. With the incorporation of new molecular technologies, theparadigm of the genetic study has changed, with a significant increase in performance and improving time to diagnostic results.The changes experienced in the reasons for consultation, diagnosesand laboratory tests carried out throughout these years reflect theimportance of the incorporation and interaction, in the same healthcare area or unit, of professionals specialized in clinical geneticsand genetic counseling, with a comprehensive genetics laboratory(including bioinformatics). (AU)

Prenatal diagnosis of severe mitochondrial diseases caused by nuclear gene defects: a study in Japan.

Prenatal diagnoses of mitochondrial diseases caused by defects in nuclear DNA (nDNA) or mitochondrial DNA have been reported in several countries except for Japan. The present study aimed to clarify the status of prenatal genetic diagnosis of mitochondrial diseases caused by nDNA defects in Japan. A comprehensive genomic analysis was performed to diagnose more than 400 patients, of which, 13 families (16 cases) had requested prenatal diagnoses. Eight cases diagnosed with wild type homozygous or heterozygous variants same as either of the heterozygous parents continued the pregnancy and delivered healthy babies. Another eight cases were diagnosed with homozygous, compound heterozygous, or hemizygous variants same as the proband. Of these, seven families chose to terminate the pregnancy, while one decided to continue the pregnancy. Neonatal- or infantile-onset mitochondrial diseases show severe phenotypes and lead to lethality. Therefore, such diseases could be candidates for prenatal diagnosis with careful genetic counseling, and prenatal testing could be a viable option for families.

Fetal early motor neuron disruption and prenatal molecular diagnosis in a severe BICD2-opathy.

BICD2 (BICD Cargo Adaptor 2, MIM*609797) mutations are associated with severe prenatal-onset forms of spinal muscular atrophy, lower extremity-predominant 2B (SMALED2B MIM 618291) or milder forms with childhood-onset (SMALED2A MIM 615290). Etiopathogenesis is not fully clarified and a wide spectrum of phenotypic presentations is reported, ranging from extreme prenatal forms with adverse outcome, to slow progressive late-onset forms. We report a fetus at 22 gestational weeks with evidence of Arthrogryposis Multiplex Congenita on ultrasound, presenting with fixed extended lower limbs and flexed upper limbs, bilateral clubfoot and absent fetal movements. A trio-based prenatal Exome Sequencing was performed, disclosing a de novo heterozygous pathogenic in frame deletion (NM_015250.3: c.1636_1638delAAT; p.Asn546del) in BICD2. After pregnancy termination, quantitative analysis on NeuN immunostained spinal cord sections of the ventral horns, revealed that neuronal density was markedly reduced compared to the one of an age-matched normal fetus and an age-matched type-I Spinal Muscular Atrophy sample, used as a comparative model. The present case, the first prenatally diagnosed and neuropathologically characterized, showed an early motor neuron loss in SMALED2B, providing further insight into the pathological basis of BICD2-opathies.

Expanded carrier screening for recessively inherited disorders: economic burden and factors in decision-making when one individual in a couple is identified as a carrier.

PURPOSE: When undergoing expanded carrier screening (ECS), couples are often screened sequentially to reduce need for a second individual's test. It is unknown how often partners of individuals found to be carriers complete the recommended testing with a sequential approach and what factors contribute to decision-making regarding partner testing. Additionally, the economic burden placed on individuals by ECS testing and its effect on partner testing has not been evaluated. METHODS: In part 1, all individuals at a university-affiliated reproductive endocrinology and infertility practice identified to be carriers of a recessively inherited mutation using the Counsyl/Foresight ECS were included. Conditions were categorized by severity according to a previously described classification system. In part 2, all individuals who underwent ECS with a single test provider between September 1, 2013 and February 1, 2020 were contacted via email to complete a confidential and anonymized online survey. RESULTS: In part 1, a total of 2061 patients were screened. 36.9% were carriers of one or more recessively inherited disorders. Twenty-seven percent of positively screened individuals did not have their partner screened. Carriers of a moderate condition had a trend towards a reduced odds for having their partner screened compared to a profound condition (OR 0.36, 95% CI 0.12-1.05, p = 0.06). Number of conditions was not predictive of subsequent partner screening (OR 0.95, 95% CI 0.72-1.25, p = 0.72). In part 2, the cost of ECS was not covered by insurance for 54.5% (103/189) and most paid over $300 out-of-pocket for testing (47.6%). The most common reason for not completing partner testing was that the results would not alter their course when seeking conception (33.3%). 73.5% of patients knew that the largest benefit of ECS comes from knowing a partner's results as well as their own. CONCLUSIONS: Not all carriers of recessively inherited disorders choose to undergo partner screening. Patients found to be carrier of more debilitating genetic disorders may be more likely to screen their reproductive partners. For many, ECS testing is not covered by insurance, and this test may impose a significant economic burden. For some patients, the results of ECS would not change what they would do when seeking conception. Providers should evaluate whether a patient's ECS result would change their treatment course prior to testing.

Novel genetic testing model: A collaboration between genetic counselors and nephrology.

Many barriers to genetic testing currently exist which delay or prevent diagnosis. These barriers include wait times, staffing, education, and cost. Specialists are able to identify patients with disease that may need genetic testing, but lack the genetics support to facilitate that testing in the most cost, time, and medically effective manner. The Nephrology Division and the Genetic Testing Stewardship Program at Nemours A.I. duPont Hospital for Children created a novel service delivery model in which nephrologists and genetic counselors collaborate in order to highlight their complementary strengths (clinical expertise of nephrologists and genetics and counseling skills of genetic counselors). This collaboration has reduced many barriers to care for our patients. This workflow facilitated the offering of genetic testing to 76 patients, with 86 tests completed over a 20-month period. Thirty-two tests were deferred. Twenty-seven patients received a diagnosis, which lead to a change in their medical management, three of whom were diagnosed by cascade family testing. Forty-two patients had a negative result and 16 patients had one or more variants of uncertain significance on testing. The inclusion of genetic counselors in the workflow is integral toward choosing the most cost and time effective genetic testing strategy, as well as providing psychosocial support to families. The genetic counselors obtain informed consent, and review genetic test results and recommendations with the patient and their family. The availability of this program to our patients increased access to genetic testing and helps to provide diagnoses and supportive care.

Pregnant women's opinions toward prenatal pretest genetic counseling in Japan.

In-person models of genetic counseling (GC) have been the common method in Japan for pregnant women to receive GC. However, recent increases in the number of pregnant women considering undergoing prenatal testing have made it challenging to retain individualized in-person care. To explore pregnant women's opinions toward pretest GC models and the ideal time duration, a self-administered questionnaire survey was conducted for women at their first prenatal visit. A total of 114 valid respondents (93.4%) were included in the analyses. Of these, 80.7% of women preferred in-person GC, followed by classroom (9.6%), group (3.5%), and telegenetic-based GC (2.6%). Women with experience in undergoing prenatal testing significantly did not prefer in-person GC (p = 0.05). Sixty-two women (54.4%) preferred a duration of 15-29 min for pretest GC sessions, followed by 30-59 min (28.9%) and <15 min (14.9%). Women's preference of ≥30 min in length was significantly associated with anhedonia, singleton pregnancies, acquaintance with people with trisomy 21, and awareness of prenatal testing. Women who were unaware of the need for agreement with the partner for prenatal testing and who did not know the average life expectancy of a trisomy 21 patient significantly preferred <15 min in length over other durations. While the majority of women preferred in-person GC for <30 min, their preferences varied by their background characteristics, experiences, attitudes, and knowledge. These findings will help establish a prenatal GC system offering a choice of GC models in Japan; however, further large-scale studies are needed to confirm these findings.

Uptake of fetal aneuploidy screening after the introduction of the non-invasive prenatal test: A national population-based register study.

INTRODUCTION: The introduction of the non-invasive prenatal test (NIPT) has shifted the prenatal screening landscape. Countries are exploring ways to integrate NIPT in their national prenatal screening programs, either as a first- or second-tier test. This study aimed to describe how the uptake of fetal aneuploidy screening changed after the introduction of NIPT as a second-tier and as a first-tier test within the national prenatal screening program of the Netherlands. MATERIAL AND METHODS: A population-based register study in the Netherlands, recording uptake of fetal aneuploidy screening. Data from all pregnant women choosing to have the first-trimester combined test (FCT) or first-tier NIPT between January 2007 and March 2019 were retrospectively collected using national registration systems. Uptake percentages for fetal aneuploidy screening (FCT and NIPT) were calculated and stratified by region and maternal age. Statistical significance was determined using trend analysis and chi-squared tests. RESULTS: Between 2007 and 2013 FCT uptake increased from 14.8% to 29.5% (P = .004). In April 2014 NIPT was introduced as a second-tier test for high-risk women after FCT (TRIDENT-1 study). FCT uptake rose from 29.5% in 2013 to 34.2% in 2015 (P < .0001). After the introduction of NIPT as a first-tier test for all women in April 2017 (TRIDENT-2 study), FCT uptake declined significantly from 35.8% in 2016 to 2.6% in 2018 (P < .0001). NIPT uptake increased to 43.4% in 2018. Regionally, NIPT uptake ranged from 31.8% to 67.9%. Total uptake (FCT and NIPT) between 2007 and 2018 increased significantly from 14.8% to 45.9% (P < .0001). However, total uptake stabilized at 46% for both years of TRIDENT-2 (April 2017-March 2019). CONCLUSIONS: An increase in total fetal aneuploidy screening uptake up to 45.9% was observed after the introduction of NIPT. Uptake appears to have stabilized within a year after introducing first-tier NIPT.

The genetic cause of intellectual deficiency and/or congenital malformations in two parental reciprocal translocation carriers and implications for assisted reproduction.

PURPOSE: To elucidate the genetic cause of intellectual deficiency and/or congenital malformations in two parental reciprocal translocation carriers and provide appropriate strategies of assisted reproductive therapy (ART). MATERIALS AND METHODS: Two similar couples having a child with global developmental delay/intellectual disability symptoms attended the Reproductive and Genetic Hospital of CITIC-Xiangya (Changsha, China) in 2017 and 2019, respectively, in order to determine the cause(s) of the conditions affecting their child and to seek ART to have a healthy baby. Both of the healthy couples were not of consanguineous marriage, denied exposure to toxicants, and had no adverse life history. This study was approved by the Institutional Ethics Committee of the Reproductive & Genetic Hospital of CITIC-Xiangya, and written informed consent was obtained from the parents. Genetic diagnoses were performed by karyotype analysis, breakpoint mapping analysis of chromosomal translocation(s), single-nucleotide polymorphism (SNP) microarray analysis, and whole-exome sequencing (WES) for the two children and different appropriate reproductive strategies were performed in the two families. RESULTS: Karyotype analysis revealed that both patients carried parental reciprocal translocations [46,XY,t(7;16)(p13;q24)pat and 46,XY,t(13;17)(q12.3;p11.2)pat, respectively]. Follow-up breakpoint mapping analysis showed no interruption of associated genes, and SNP microarray analysis identified no significant copy number variations (CNVs) in the two patients. Moreover, WES results revealed that patients 1 and 2 harbored candidate compound heterozygous mutations of MCOLN1 [c.195G>C (p.K65N) and c.1061G>A (p.W354*)] and MCPH1 [c.877A>G (p.S293G) and c.1869_1870delAT (p.C624*)], respectively, that were inherited from their parents and not previously reported. Furthermore, the parents of patient 1 obtained 10 embryos during ART cycle, and an embryo of normal karyotype and non-carrier of observed MCOLN1 mutations according to preimplantation genetic testing for structural rearrangement and monogenic defect was successfully transferred, resulting in the birth of a healthy boy. The parents of patient 2 chose to undergo ART with donor sperm to reduce the risk of recurrence. CONCLUSIONS: Systematic genetic diagnosis of two carriers of inherited chromosomal translocations accompanied by clinical phenotypes revealed their cause of disease, which was critical for genetic counseling and further ART for these families.

Non-Invasive Prenatal Testing: Current Perspectives and Future Challenges.

Fetal aneuploidies are among the most common causes of miscarriages, perinatal mortality and neurodevelopmental impairment. During the last 70 years, many efforts have been made in order to improve prenatal diagnosis and prenatal screening of these conditions. Recently, the use of cell-free fetal DNA (cff-DNA) testing has been increasingly used in different countries, representing an opportunity for non-invasive prenatal screening of pregnant women. The aim of this narrative review is to describe the state of the art and the main strengths and limitations of this test for prenatal screening of fetal aneuploidies.

Genetic testing for inherited retinal degenerations: Triumphs and tribulations.

Inherited retinal degenerations (IRDs) are a genotypically and phenotypically diverse group of conditions. Great strides have been made toward identifying the genetic basis for these conditions over the last 30 years-more than 270 different genes involved in syndromic and nonsyndromic forms of retinal dystrophies have now been identified. The identification of these genes and the improvement of clinical laboratory techniques have led to the identification of the genetic basis of disease in 56-76% of patients with IRDs through next generation sequencing and copy number variant analysis. Genetic testing is an essential part of clinical care for patients affected with IRDs and is required to confirm the diagnosis, understand the inheritance of the condition, and determine eligibility for gene-specific treatments or clinical trials. Despite the success achieved in determining the genetic cause of these conditions, several challenges remain, which must be considered when providing genetic testing and genetic counseling to patients. For this reason, an integrated team of ophthalmic and genetic clinicians who are familiar with these challenges is necessary to provide optimal comprehensive care to these patients.

Family history risk assessment by a genetic counselor is a critical step in screening all patients in the ART clinic.

The family history is the cornerstone of the genetic risk assessment. Taking a detailed family history helps ensure that important genetic information is not overlooked and that any appropriate testing and/or information is provided to the patient prior to pregnancy. Guidelines from the American Society for Reproductive Medicine (ASRM) suggest a review of personal and family history of genetic disease and prior genetic test results that may affect the course of treatment, with patients being counseled about additional genetic testing that may be indicated before starting treatment relating to their personal or family history. When issues arise as a result of this evaluation, referral to a genetics specialist is recommended. As the following cases demonstrate, implementation of a routine genetic counseling screening program for all patients using assisted reproductive technology (ART) provides immense benefits so that important indications for referral to a genetic counselor are not missed.

Early-onset nucleotide excision repair disorders with neurological impairment: Clues for early diagnosis and prognostic counseling.

Nucleotide excision repair associated diseases comprise overlapping phenotypes and a wide range of outcomes. The early stages still remain under-investigated and underdiagnosed, even although an early recognition of the first symptoms is of utmost importance for appropriate care and genetic counseling. We systematically collected clinical and molecular data from the literature and from newly diagnosed NER patients with neurological impairment, presenting clinical symptoms before the age of 12 months, including foetal cases. One hundred and eighty-five patients were included, 13 with specific symptoms during foetal life. Arthrogryposis, microcephaly, cataracts, and skin anomalies are the most frequently reported signs in early subtypes. Non ERCC6/CSB or ERCC8/CSA genes are overrepresented compared to later onset cohorts: 19% patients of this cohort presented variants in ERCC1, ERCC2/XPD, ERCC3/XPB or ERCC5/XPG. ERCC5/XPG is even the most frequently involved gene in foetal cases (10/13 cases, [4/7 families]). In this cohort, the mutated gene, the age of onset, the type of disease, severe global developmental delay, IUGR and skin anomalies were associated with earlier death. This large survey focuses on specific symptoms that should attract the attention of clinicians towards early-onset NER diagnosis in foetal and neonatal period, without waiting for the completeness of classical criteria.

Health Supervision for People With Achondroplasia.

Achondroplasia is the most common short-stature skeletal dysplasia, additionally marked by rhizomelia, macrocephaly, midface hypoplasia, and normal cognition. Potential medical complications associated with achondroplasia include lower extremity long bone bowing, middle-ear dysfunction, obstructive sleep apnea, and, more rarely, cervicomedullary compression, hydrocephalus, thoracolumbar kyphosis, and central sleep apnea. This is the second revision to the original 1995 health supervision guidance from the American Academy of Pediatrics for caring for patients with achondroplasia. Although many of the previously published recommendations remain appropriate for contemporary medical care, this document highlights interval advancements in the clinical methods available to monitor for complications associated with achondroplasia. This document is intended to provide guidance for health care providers to help identify individual patients at high risk of developing serious sequelae and to enable intervention before complications develop.

Telehealth technology: Reducing barriers for rural residents seeking genetic counseling.

Many rural residents do not receive genetic counseling or testing when needed because of health care access barriers, such as lack of providers in rural areas and the requirement for rural residents to travel to larger cities for these services. Telehealth technology can reduce these barriers by allowing rural residents to receive genetic counseling through a two-way interactive audio/video secure connection in a local clinic setting or in their homes. Telegenetics is a satisfactory solution for both patient and provider and provides benefits for rural patients despite ethical, legal, and reimbursement considerations.