Clinical whole-exome sequencing is increasingly used for diagnostic evaluation of patients with suspected genetic disorders.
To perform clinical whole-exome sequencing and report (1) the rate of ...molecular diagnosis among phenotypic groups, (2) the spectrum of genetic alterations contributing to disease, and (3) the prevalence of medically actionable incidental findings such as FBN1 mutations causing Marfan syndrome.
Observational study of 2000 consecutive patients with clinical whole-exome sequencing analyzed between June 2012 and August 2014. Whole-exome sequencing tests were performed at a clinical genetics laboratory in the United States. Results were reported by clinical molecular geneticists certified by the American Board of Medical Genetics and Genomics. Tests were ordered by the patient's physician. The patients were primarily pediatric (1756 88%; mean age, 6 years; 888 females 44%, 1101 males 55%, and 11 fetuses 1% gender unknown), demonstrating diverse clinical manifestations most often including nervous system dysfunction such as developmental delay.
Whole-exome sequencing diagnosis rate overall and by phenotypic category, mode of inheritance, spectrum of genetic events, and reporting of incidental findings.
A molecular diagnosis was reported for 504 patients (25.2%) with 58% of the diagnostic mutations not previously reported. Molecular diagnosis rates for each phenotypic category were 143/526 (27.2%; 95% CI, 23.5%-31.2%) for the neurological group, 282/1147 (24.6%; 95% CI, 22.1%-27.2%) for the neurological plus other organ systems group, 30/83 (36.1%; 95% CI, 26.1%-47.5%) for the specific neurological group, and 49/244 (20.1%; 95% CI, 15.6%-25.8%) for the nonneurological group. The Mendelian disease patterns of the 527 molecular diagnoses included 280 (53.1%) autosomal dominant, 181 (34.3%) autosomal recessive (including 5 with uniparental disomy), 65 (12.3%) X-linked, and 1 (0.2%) mitochondrial. Of 504 patients with a molecular diagnosis, 23 (4.6%) had blended phenotypes resulting from 2 single gene defects. About 30% of the positive cases harbored mutations in disease genes reported since 2011. There were 95 medically actionable incidental findings in genes unrelated to the phenotype but with immediate implications for management in 92 patients (4.6%), including 59 patients (3%) with mutations in genes recommended for reporting by the American College of Medical Genetics and Genomics.
Whole-exome sequencing provided a potential molecular diagnosis for 25% of a large cohort of patients referred for evaluation of suspected genetic conditions, including detection of rare genetic events and new mutations contributing to disease. The yield of whole-exome sequencing may offer advantages over traditional molecular diagnostic approaches in certain patients.
Whole-exome sequencing is a diagnostic approach for the identification of molecular defects in patients with suspected genetic disorders.
We developed technical, bioinformatic, interpretive, and ...validation pipelines for whole-exome sequencing in a certified clinical laboratory to identify sequence variants underlying disease phenotypes in patients.
We present data on the first 250 probands for whom referring physicians ordered whole-exome sequencing. Patients presented with a range of phenotypes suggesting potential genetic causes. Approximately 80% were children with neurologic phenotypes. Insurance coverage was similar to that for established genetic tests. We identified 86 mutated alleles that were highly likely to be causative in 62 of the 250 patients, achieving a 25% molecular diagnostic rate (95% confidence interval, 20 to 31). Among the 62 patients, 33 had autosomal dominant disease, 16 had autosomal recessive disease, and 9 had X-linked disease. A total of 4 probands received two nonoverlapping molecular diagnoses, which potentially challenged the clinical diagnosis that had been made on the basis of history and physical examination. A total of 83% of the autosomal dominant mutant alleles and 40% of the X-linked mutant alleles occurred de novo. Recurrent clinical phenotypes occurred in patients with mutations that were highly likely to be causative in the same genes and in different genes responsible for genetically heterogeneous disorders.
Whole-exome sequencing identified the underlying genetic defect in 25% of consecutive patients referred for evaluation of a possible genetic condition. (Funded by the National Human Genome Research Institute.).
While congenital malformations and genetic diseases are a leading cause of early infant death, to our knowledge, the contribution of single-gene disorders in this group is undetermined.
To determine ...the diagnostic yield and use of clinical exome sequencing in critically ill infants.
Clinical exome sequencing was performed for 278 unrelated infants within the first 100 days of life who were admitted to Texas Children's Hospital in Houston, Texas, during a 5-year period between December 2011 and January 2017. Exome sequencing types included proband exome, trio exome, and critical trio exome, a rapid genomic assay for seriously ill infants.
Indications for testing, diagnostic yield of clinical exome sequencing, turnaround time, molecular findings, patient age at diagnosis, and effect on medical management among a group of critically ill infants who were suspected to have genetic disorders.
The mean (SEM) age for infants participating in the study was 28.5 (1.7) days; of these, the mean (SEM) age was 29.0 (2.2) days for infants undergoing proband exome sequencing, 31.5 (3.9) days for trio exome, and 22.7 (3.9) days for critical trio exome. Clinical indications for exome sequencing included a range of medical concerns. Overall, a molecular diagnosis was achieved in 102 infants (36.7%) by clinical exome sequencing, with relatively low yield for cardiovascular abnormalities. The diagnosis affected medical management for 53 infants (52.0%) and had a substantial effect on informed redirection of care, initiation of new subspecialist care, medication/dietary modifications, and furthering life-saving procedures in select patients. Critical trio exome sequencing revealed a molecular diagnosis in 32 of 63 infants (50.8%) at a mean (SEM) of 33.1 (5.6) days of life with a mean (SEM) turnaround time of 13.0 (0.4) days. Clinical care was altered by the diagnosis in 23 of 32 patients (71.9%). The diagnostic yield, patient age at diagnosis, and medical effect in the group that underwent critical trio exome sequencing were significantly different compared with the group who underwent regular exome testing. For deceased infants (n = 81), genetic disorders were molecularly diagnosed in 39 (48.1%) by exome sequencing, with implications for recurrence risk counseling.
Exome sequencing is a powerful tool for the diagnostic evaluation of critically ill infants with suspected monogenic disorders in the neonatal and pediatric intensive care units and its use has a notable effect on clinical decision making.
Exome sequencing is now being incorporated into clinical care for pediatric and adult populations, but its integration into prenatal diagnosis has been more limited. One reason for this is the ...paucity of information about the clinical utility of exome sequencing in the prenatal setting.
We retrospectively reviewed indications, results, time to results (turnaround time, TAT), and impact of exome results for 146 consecutive "fetal exomes" performed in a clinical diagnostic laboratory between March 2012 and November 2017. We define a fetal exome as one performed on a sample obtained from a fetus or a product of conception with at least one structural anomaly detected by prenatal imaging or autopsy. Statistical comparisons were performed using Fisher's exact test.
Prenatal exome yielded an overall molecular diagnostic rate of 32% (n = 46/146). Of the 46 molecular diagnoses, 50% were autosomal dominant disorders (n = 23/46), 41% were autosomal recessive disorders (n = 19/46), and 9% were X-linked disorders (n = 4/46). The molecular diagnostic rate was highest for fetuses with anomalies affecting multiple organ systems and for fetuses with craniofacial anomalies. Out of 146 cases, a prenatal trio exome option designed for ongoing pregnancies was performed on 62 fetal specimens, resulting in a diagnostic yield of 35% with an average TAT of 14 days for initial reporting (excluding tissue culture time). The molecular diagnoses led to refined recurrence risk estimates, altered medical management, and informed reproductive planning for families.
Exome sequencing is a useful diagnostic tool when fetal structural anomalies suggest a genetic etiology, but other standard prenatal genetic tests did not provide a diagnosis.
SON is a key component of the spliceosomal complex and a critical mediator of constitutive and alternative splicing. Additionally, SON has been shown to influence cell-cycle progression, genomic ...integrity, and maintenance of pluripotency in stem cell populations. The clear functional relevance of SON in coordinating essential cellular processes and its presence in diverse human tissues suggests that intact SON might be crucial for normal growth and development. However, the phenotypic effects of deleterious germline variants in SON have not been clearly defined. Herein, we describe seven unrelated individuals with de novo variants in SON and propose that deleterious variants in SON are associated with a severe multisystem disorder characterized by developmental delay, persistent feeding difficulties, and congenital malformations, including brain anomalies.
Traumatic hemorrhage is the most common cause of preventable death in civilian and military trauma. Early identification of pediatric life-threatening hemorrhage is challenging. There is no accepted ...clinical critical administration threshold (CAT) in children for activating massive transfusion protocols.
Children 0 to 17 years old who received any transfusion in the first 24 hours after injury between 2010 and 2019 were included. The type, volume, and time of administration for each product were recorded. The greatest volume of weight-adjusted products transfused within 1 hour was calculated. The cut point for the number of products that maximized sensitivity and specificity to predict in-hospital mortality, need for urgent surgery, and second life-threatening bleeding episode was determined using Youden's index. A binary variable (CAT+) was generated using this threshold for inclusion in a multivariable logistic regression model.
In total, 287 patients were included. The median (interquartile range) age was 6 (2-14) years, 60% were males, 83% sustained blunt trauma, and the median (interquartile range) Injury Severity Score was 26 (17-35). The optimal cutoff to define CAT+ was >20 mL/kg of product; this optimized test characteristics for mortality (sensitivity, 70%; specificity, 77%), need for urgent hemorrhage control procedure (sensitivity, 65%; specificity, 74%). and second bleeding episode (sensitivity, 77%; specificity, 74%). There were 93 children (32%) who were CAT+. On multivariate regression, being CAT+ was associated with 3.4 increased odds of mortality (95% confidence interval, 1.67-6.89; p = 0.001) after controlling for age, hypotension, Injury Severity Score, and Glasgow Coma Scale. For every unit of product administered, there was a 10% increased risk of mortality (odds ratio, 1.1; p < 0.001).
Transfusion of more than 20 mL/kg of any blood product within an hour should be used as a threshold for activating massive transfusion protocols in children. Children who meet this CAT are at high risk of mortality and need for interventions; this population may benefit from targeted, timely, and aggressive hemostatic resuscitation.
Therapeutic/Care Management; Level III.
Mississippi has one of the highest rates of HIV in the United States but low PrEP uptake. Understanding patterns of PrEP use can improve PrEP initiation and persistence.
This is a mixed-method ...evaluation of a PrEP program in Jackson, Mississippi. Between November 2018-December 2019, clients at high risk for HIV attending a non-clinical testing site were referred to a pharmacist for same-day PrEP initiation. The pharmacist provided a 90-day PrEP prescription and scheduled a follow-up clinical appointment within three months. We linked client records from this visit to electronic health records from the two largest PrEP clinics in Jackson to determine linkage into ongoing clinical care. We identified four distinct PrEP use patterns, which we used for qualitative interview sampling: 1) filled a prescription and linked into care within three months; 2) filled a prescription and linked into care after three months; 3) filled a prescription and never linked into care; and 4) never filled a prescription. In 2021, we purposively sampled patients in these four groups for individual interviews to ascertain barriers and facilitators to PrEP initiation and persistence, using guides informed by the Theory of Planned Behavior.
There were 121 clients evaluated for PrEP; all were given a prescription. One-third were less than 25 years old, 77% were Black, and 59% were cisgender men who have sex with men. One-quarter (26%) never filled their PrEP prescription, 44% picked up the prescription but never linked into clinical care, 12% linked into care at some point after three months (resulting in a gap in PrEP coverage), and 18% linked into care within 3 months. We interviewed 26 of 121 clients. Qualitative data revealed that cost, stigmas related to sexuality and HIV, misinformation about PrEP, and perceived side effects were barriers to uptake and persistence. Individuals' desire to stay healthy and the support of PrEP clinic staff were facilitators.
The majority of individuals given a same-day PrEP prescription either never started PrEP or stopped PrEP within the first three months. Addressing noted barriers of stigma and misinformation and reducing structural barriers may increase PrEP initiation and persistence.
Reanalysis of Clinical Exome Sequencing Data Liu, Pengfei; Meng, Linyan; Normand, Elizabeth A ...
The New England journal of medicine,
06/2019, Letnik:
380, Številka:
25
Journal Article
Optimal hemostatic resuscitation in pediatric trauma is not well defined.
To assess the association of prehospital blood transfusion (PHT) with outcomes in injured children.
This retrospective cohort ...study of the Pennsylvania Trauma Systems Foundation database included children aged 0 to 17 years old who received a PHT or emergency department blood transfusion (EDT) from January 2009 and December 2019. Interfacility transfers and isolated burn mechanism were excluded. Analysis took place between November 2022 and January 2023.
Receipt of a blood product transfusion in the prehospital setting compared with the emergency department.
The primary outcome was 24-hour mortality. A 3:1 propensity score match was developed balancing for age, injury mechanism, shock index, and prehospital Glasgow Comma Scale score. A mixed-effects logistic regression was performed in the matched cohort further accounting for patient sex, Injury Severity Score, insurance status, and potential center-level heterogeneity. Secondary outcomes included in-hospital mortality and complications.
Of 559 children included, 70 (13%) received prehospital transfusions. In the unmatched cohort, the PHT and EDT groups had comparable age (median IQR, 47 9-16 vs 14 9-17 years), sex (46 66% vs 337 69% were male), and insurance status (42 60% vs 245 50%). The PHT group had higher rates of shock (39 55% vs 204 42%) and blunt trauma mechanism (57 81% vs 277 57%) and lower median (IQR) Injury Severity Score (14 5-29 vs 25 16-36). Propensity matching resulted in a weighted cohort of 207 children, including 68 of 70 recipients of PHT, and produced well-balanced groups. Both 24-hour (11 16% vs 38 27%) and in-hospital mortality (14 21% vs 44 32%) were lower in the PHT cohort compared with the EDT cohort, respectively; there was no difference in in-hospital complications. Mixed-effects logistic regression in the postmatched group adjusting for the confounders listed above found PHT was associated with a significant reduction in 24-hour (adjusted odds ratio, 0.46; 95% CI, 0.23-0.91) and in-hospital mortality (adjusted odds ratio, 0.51; 95% CI, 0.27-0.97) compared with EDT. The number needed to transfuse in the prehospital setting to save 1 child's life was 5 (95% CI, 3-10).
In this study, prehospital transfusion was associated with lower rates of mortality compared with transfusion on arrival to the emergency department, suggesting bleeding pediatric patients may benefit from early hemostatic resuscitation. Further prospective studies are warranted. Although the logistics of prehospital blood product programs are complex, strategies to shift hemostatic resuscitation toward the immediate postinjury period should be pursued.
The role of age in mediating coagulation characteristics in injured children is not well defined. We hypothesize thromboelastography (TEG) profiles are unique across pediatric age groups.
Consecutive ...trauma patients younger than 18 years from a Level I pediatric trauma center database from 2016 to 2020 with TEG obtained on arrival to the trauma bay were identified. Children were categorized by age according to the National Institute of Child Health and Human Development categories (infant, ≤1 year; toddler, 1-2 years; early childhood, 3-5 years; older childhood, 6-11 years; adolescent, 12-17 years). Thromboelastography values were compared across age groups using Kruskal-Wallis and Dunn's tests. Analysis of covariance was performed controlling for sex, Injury Severity Score (ISS), arrival Glasgow Coma Scale (GCS) score, shock, and mechanism of injury.
In total, 726 subjects were identified; 69% male, median (interquartile range IQR) ISS = 12 (5-25), and 83% had a blunt mechanism. On univariate analysis, there were significant differences in TEG α-angle ( p < 0.001), MA ( p = 0.004), and fibrinolysis 30 minutes after MA (LY30) ( p = 0.01) between groups. In post hoc tests, the infant group had significantly greater α-angle (median, 77; IQR, 71-79) and MA (median, 64; IQR, 59-70) compared with other groups, while the adolescent group had significantly lower α-angle (median, 71; IQR, 67-74), MA (median, 60; IQR, 56-64), and LY30 (median, 0.8; IQR, 0.2-1.9) compared with other groups. There were no significant differences between toddler, early childhood, and middle childhood groups. On multivariate analysis, the relationship between age group and TEG values (α-angle, MA, and LY30) persisted after controlling for sex, ISS, GCS, shock, and mechanism of injury.
Age-associated differences in TEG profiles across pediatric age groups exist. Further pediatric-specific research is required to assess whether the unique profiles at extremes of childhood translate to differential clinical outcomes or responses to therapies in injured children.
Prognostic and Epidemiological; Level IV.
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