Introducción al filtrado, análisis y curación de variantes genéticas en pacientes con Discapacidad Intelectual / Introduction to filtering, analysis and curation of genetic variants in patients with Intellectual Disability

Resumen Actualmente la secuenciación del exoma completo (WES; Whole-exome sequencing) mediante la técnica NGS (Next-generation sequencing) es uno de los estudios genéticos más solicitados dentro del abordaje de pacientes con Discapacidad Intelectual con o sin otras anomalías. Al igual que con otros proce dimientos y estudios clínicos, es conveniente que los médicos prescriptores tengan una comprensión clara de los alcances y limitaciones del uso de WES, del proceso de análisis de las variantes genéticas identificadas, así como de aspectos a evaluar acerca de la calidad y estructura de los informes de los estudios de NGS, con el objetivo de que puedan interpretar mejor los resultados de un estudio y plantear de la mejor manera la correlación de los mismos con la clínica observada.

Abstract Currently, Whole exome sequencing (WES) using NGS (Next-generation sequencing) technology is one of the most requested genetic studies within the approach of patients with intellectual disability with or without other anomalies. As with other procedures and clinical studies, it is convenient for prescribing physicians to have a clear understanding of the scope and limitations of the use of WES, the analysis process of the genetic variants identified, as well as aspects to be evaluated regarding quality and structure of the reports of the NGS studies, with the aim that they can better interpret the results of a study, evaluate its quality, and propose in the best way the correlation of the same with the observed phenotype.

[Introduction to filtering, analysis and curation of genetic variants in patients with intellectual disability]. / Introducción al filtrado, análisis y curación de variantes genéticas en pacientes con discapacidad intelectual.

Currently, Whole exome sequencing (WES) using NGS (Next-generation sequencing) technology is one of the most requested genetic studies within the approach of patients with intellectual disability with or without other anomalies. As with other procedures and clinical studies, it is convenient for prescribing physicians to have a clear understanding of the scope and limitations of the use of WES, the analysis process of the genetic variants identified, as well as aspects to be evaluated regarding quality and structure of the reports of the NGS studies, with the aim that they can better interpret the results of a study, evaluate its quality, and propose in the best way the correlation of the same with the observed phenotype.

Actualmente la secuenciación del exoma completo (WES; Whole-exome sequencing) mediante la técnica NGS (Next-generation sequencing) es uno de los estudios genéticos más solicitados dentro del abordaje de pacientes con Discapacidad Intelectual con o sin otras anomalías. Al igual que con otros procedimientos y estudios clínicos, es conveniente que los médicos prescriptores tengan una comprensión clara de los alcances y limitaciones del uso de WES, del proceso de análisis de las variantes genéticas identificadas, así como de aspectos a evaluar acerca de la calidad y estructura de los informes de los estudios de NGS, con el objetivo de que puedan interpretar mejor los resultados de un estudio y plantear de la mejor manera la correlación de los mismos con la clínica observada.

Prenatal Diagnosis of Vasa Previa by Routine Transvaginal Color Doppler.

The prenatal diagnosis of vasa previa is essential to achieving a safe delivery in patients who suffer from the condition. Transvaginal ultrasound with color Doppler performed at the time of a routine mid-trimester ultrasound is a valuable tool in terms of achieving a timely and accurate diagnosis of vasa previa.

Congenital dacryocystocele: sonographic evaluation of 11 cases.

PURPOSE: To report prenatal sonographic findings of congenital dacryocystocele. METHODS: The medical records of all cases diagnosed with congenital dacryocystocele at a tertiary care center from 2003 to 2015 were reviewed retrospectively. RESULTS: Eleven cases of congenital dacryocystocele were analyzed. No accompanying fetal anatomic anomalies where detected. Mean maternal age at evaluation was 22 years of age (range, 17-32 years). Four of 10 cases were primigravidas. The mean gestational age at evaluation was 32.6 weeks' gestational age. Ten out of 11 cases occurred in female fetuses (91%). Of the 11, 10 cases were unilateral and 1 was bilateral. The mean diameter at evaluation was 5.1 mm. Spontaneous resolution occurred in 2 cases (18%). In the remaining 9 fetuses, postnatal diagnosis of dacryocystocele were confirmed by an ophthalmologist evaluation. CONCLUSIONS: Prenatally diagnosed congenital dacryocystocele may undergo spontaneous resolution before birth. However, a better understanding of the prenatal sonographic findings can help to appropriately orient parents of potentially affected fetuses. Referral to a pediatrician and pediatric ophthalmologist may be considered for complete evaluation and postnatal management.

INSIG2 rs7566605 single nucleotide variant and global DNA methylation index levels are associated with weight loss in a personalized weight reduction program.

Single nucleotide polymorphisms associated with lipid metabolism and energy balance are implicated in the weight loss response caused by nutritional interventions. Diet­induced weight loss is also associated with differential global DNA methylation. DNA methylation has been proposed as a predictive biomarker for weight loss response. Personalized biomarkers for successful weight loss may inform clinical decisions when deciding between behavioral and surgical weight loss interventions. The aim of the present study was to investigate the association between global DNA methylation, genetic variants associated with energy balance and lipid metabolism, and weight loss following a non­surgical weight loss regimen. The present study included 105 obese participants that were enrolled in a personalized weight loss program based on their allelic composition of the following five energy balance and lipid metabolism­associated loci: Near insulin­induced gene 2 (INSIG2); melanocortin 4 receptor; adrenoceptor ß2; apolipoprotein A5; and G­protein subunit ß3. The present study investigated the association between a global DNA methylation index (GDMI), the allelic composition of the five energy balance and lipid metabolism­associated loci, and weight loss during a 12 month program, after controlling for age, sex and body mass index (BMI). The results demonstrated a significant association between the GDMI and near INSIG2 locus, after adjusting for BMI and weight loss, and significant trends were observed when stratifying by gender. In conclusion, a combination of genetic and epigenetic biomarkers may be used to design personalized weight loss interventions, enabling adherence and ensuring improved outcomes for obesity treatment programs. Precision weight loss programs designed based on molecular information may enable the creation of personalized interventions for patients, that use genomic biomarkers for treatment design and for treatment adherence monitoring, thus improving response to treatment.

Zika Virus Infection in Pregnancy: Maternal, Fetal, and Neonatal Considerations.

An infection with the Zika virus (ZIKV) is usually mild, with nonspecific symptoms and most often asymptomatic. However, because of its causal relationship with severe congenital malformations, the ZIKV epidemic became an imperative for mobilization, renewed strategies for vector control, and biomedical research. A congenital Zika syndrome (CZS) has been characterized with 5 distinctive features that focus on brain development abnormalities (including microcephaly and brain calcifications), retinal manifestations, and defects on extremities including congenital contractures and hypertonia. The CZS could be just "the tip of the iceberg", pending the documentation of a spectrum of disease that could manifest later in life, from mild dysfunction to severe disease. It will be a matter of time for neurodevelopmental abnormalities, learning disabilities, and other unknown but yet-to-be-described outcomes to be associated with intrauterine ZIKV infection. In addition, ZIKV infection during pregnancy has been associated with other adverse outcomes. Reports mostly include ZIKV-affected pregnancies, and it will be difficult to clearly establish causality without appropriate control groups. We are summarizing some of the known or reported consequences of such infection during pregnancy. Women of reproductive age and particularly pregnant women are the most vulnerable to the adverse consequences of the ZIKV epidemic. Vector control programs need to be expanded to curtail new infections. Research is needed to develop safe and effective treatments, a preventive or therapeutic vaccine, and specific and sensitive tests and to diagnose and identify correlates of long-term immunity. Vaccines and treatments should be safe to be used in pregnancy. To do nothing would allow thousands of pregnant women to expose their fetuses to an infection that causes birth defects and other problems. Prenatal diagnosis technology development is necessary to be able to predict or diagnose adverse fetal outcomes related to ZIKV. Moreover, these tests should be used in a manner similar to the testing/screening method for neural tube defects and common chromosomal anomalies during prenatal care.

Rapid Resolution of Polyhydramnios Foretells Circulatory Collapse for the Donor Twin in Feto-Fetal Transfusion Syndrome.

Feto-fetal transfusion syndrome is a pathological process unique to diamniotic monochorionic pregnancies. It is the consequence of an unbalanced fetal blood flow through communicating vessels within a shared placenta. When it occurs, a polyuric, hypervolemic recipient twin co-exists with a hypovolemic oliguric donor. The presence of polyhydramnios or oligohydramnios is considered a poor prognostic indicator, whereas normal amniotic fluid volumes indicate a lack of clinically significant twintwin transfusion. In addition, the spontaneous normalization of amniotic fluid volume is usually seen as a favorable prognostic sign. Here, however, we present a case of feto-fetal transfusion in a 31 year-old primigravida at 19 week, in which the spontaneous normalization of amniotic fluid volume in the recipient twin preceded the death of the donor.

Prevalence of recurrent pathogenic microdeletions and microduplications in over 9500 pregnancies.

OBJECTIVES: The implementation of chromosomal microarray analysis (CMA) in prenatal testing for all patients has not achieved a consensus. Technical alternatives such as Prenatal BACs-on-Beads(TM) (PNBoBs(TM) ) have thus been applied. The aim of this study was to provide the frequencies of the submicroscopic defects detectable by PNBoBs(TM) under different prenatal indications. METHODS: A total of 9648 prenatal samples were prospectively analyzed by karyotyping plus PNBoBs(TM) and classified by prenatal indication. The frequencies of the genomic defects and their 95%CIs were calculated for each indication. RESULTS: The overall incidence of cryptic imbalances was 0.7%. The majority involved the DiGeorge syndrome critical region (DGS). The additional diagnostic yield of PNBoBs(TM) in the population with a low a priori risk was 1/298. The prevalences of DGS microdeletion and microduplication in the low-risk population were 1/992 and 1/850, respectively. CONCLUSIONS: The constant a priori risk for common pathogenic cryptic imbalances detected by this technology is estimated to be ~0.3%. A prevalence higher than that previously estimated was found for the 22q11.2 microdeletion. Their frequencies were independent of maternal age. These data have implications for cell-free DNA screening tests design and justify prenatal screening for 22q11 deletion, as early recognition of DGS improves its prognosis.

Cerebral palsy, epilepsy, and severe intellectual disability in a patient with 3q29 microduplication syndrome.

Interstitial microduplication of 3q29 has been recently described. Individuals with this syndrome have widely variable phenotypes. We describe the first clinical case with a 1.607 Mb duplication at 3q29 (chr3: 195,731,956-197,339,329), accompanied by severe intellectual disability, epilepsy, and cerebral palsy. This duplication involves 22 genes; PAK2, DLG1, BDH1, and FBXO45 are implicated in neuronal development and synaptic function and could play an important role in this syndrome. We propose considering genetic studies, particularly array comparative genomic hybridization, in patients with epilepsy and/or cerebral palsy of unknown etiology when dysmorphic features are present.

Pregnancy after liver transplantation.

UNLABELLED: Several reports on liver transplantation and pregnancy have been published recently. Uncertainty remains regarding appropriate management of these patients. METHODS: The study included pregnant women of all ages with liver transplant referred to our center. A total of eight patients were identified and qualified for our study. The following variables were obtained: age, date of liver transplantation, date of conception, reasons for liver transplantation, type of immunosuppressive therapy, complications during pregnancy, gestational age at birth, birth weight, mode of delivery, the interval of time from liver transplantation to conception and co-morbidity. RESULTS: The mean age of our population was 24 years. Four of the eight were nulliparous. The mean time interval from transplantation to pregnancy was eight years. The indication for liver transplantation in 75% of patients was autoimmune hepatitis. Two cases were associated with viral hepatitis. Combination therapy with more than one immunosuppressant was given to 75% of patients. The most prevalent complication was pyelonephritis in (38%), followed by gestational thrombocytopenia and preeclampsia. Most deliveries (75%) were vaginal and at term (88%). The median for gestational age was 39 weeks. The median birth weight was 2,898 grams. CONCLUSIONS: This study proves that successful and uneventful pregnancies are likely in liver transplant patients under optimal obstetric management.

Effectiveness and safety of lidocaine in the induction of fetal cardiac asystole for second trimester pregnany termination.

UNLABELLED: The presence of a major congenital anomaly is a frequent indication for late termination of pregnancy. The possibility of the fetus being born alive is significant, thus, feticide prior to the procedure is desirable. The purpose of this study was to assess the safety and efficacy of lidocaine 1% as a feticidal agent prior to second trimester termination of pregnancy. METHODS: We conducted a chart review of all patients who underwent a second trimester termination of pregnancy at our institution between March 2009 and June 2012. We collected data regarding the indication for the termination procedure, gestational age, site of lidocaine injection, dosage of lidocaine, need for additional to produce asystole, and maternal complications. RESULTS: We identified 54 patients who underwent second trimester termination following injection with lidocaine. Forty-six cases (85%) were done for major fetal anomalies and 8 cases (15%) were for maternal indications. The mean gestational age was 22 weeks (SD = 2.3). The mean volume of lidocaine 1% injected was 10.1 mL (range: 5-40 mL). Asystole was achieved in 1-2 minutes following intracardiac administration. Intracardiac injection was successful in 45/46 (98%) of cases. Intrathoracic administration was successful in 5/6 (83%). This approach was chosen when cardiac puncture was not effective. Two fetuses receiving an initial intraabdominal or umbilical vein injection required additional doses of intracardiac lidocaine to produce asystole. There were no maternal complications. CONCLUSIONS: Intracardiac administration of lidocaine is an effective method to induce cardiac asystole for second trimester pregnancy termination. Extra-cardiac injection, however, is less effective.

Prenatal diagnosis of a vein of Galen aneurysmal malformation using color Doppler ultrasound: a case report.

Vein of Galen aneurysms are a rare and complex vascular malformation of the brain. Their prevalence is somewhat less than 1 in 25,000 deliveries. Common associated anomalies include ventriculomegaly, cardiomegaly secondary to high cardiac output and enlarged neck vessels, the later being an almost pathognomonic sign. The prognosis for these neonates is poor with a mortality rate of 50% and a high risk for neurologic sequelae. Color flow Doppler studies of the fetal brain vasculature are a reliable method for diagnostic purposes. In this paper we present a case of a vein of Galen malformation diagnosed prenatally at 33 weeks of gestation using both 2D and color Doppler ultrasound modalities.

Chorioangioma: an uncommon cause of hydramnios and consequent preterm labor in second trimester of pregnancy.

Placental chorioangiomas are relatively common benign placental tumors occurring with an incidence of approximately 1% of histologically studied placentas. However, they show clinical manifestations in very rare pregnancies usually at a median gestational age of 28 weeks. Our report presents an interesting and rare case of severe hydramnios with consequent preterm labor and delivery in the second trimester leading to neonatal death due to placental chorioangioma. An earlier diagnosis could have led to closer monitoring and prevention of the development of severe hydramnios with resultant preterm labor.

Antenatal screening for Down syndrome with special considerations in the Puerto Rican population.

Down syndrome is the most studied chromosomal abnormality, and the risk of having a child with Down syndrome increases as maternal age increases. The prevalence of Down syndrome has been increasing in the last decade because more women older than 35 years of age are having children. In recent decades, the rate of identification of fetal anomalies in the uterus has substantially increased. Diagnostically speaking, serious concerns yet remain within the obstetrical community regarding who should be recommended for invasive procedures. The FASTER, SURUSS, and BUN studies have attempted to address this issue. In the United States, the quadruple screen for Down syndrome (hcG, AFP, estriol, and inhibin-A) is the most commonly used test today. During the first trimester, the nuchal translucency measurement combined with serum markers hcG and PAPP-A (pregnancy-associated plasma protein-A) results in high detection rates and low false-positive rates. For Down syndrome screening, new methods of evaluation have been proposed; among these are integrated, sequential, and contingent modalities. Different trials have demonstrated that first-trimester screening for Down syndrome is very effective, but all conclude that combining screening during both trimesters allows for lower false-positive values and higher detection rates. In Puerto Rico, in spite of the fact that a large proportion of the population undergoes serum screening, the rate of Down syndrome live births remains steady. One important aspect that appears to limit prenatal diagnosis of Down syndrome in our population is a poor acceptance rate of diagnostic testing techniques such as amniocentesis. Also, a limited efficiency in the implementation of these screening methods as well as their diagnostic success has been observed for our patient population.

Seasonal variations in the incidence of some congenital anomalies in Puerto Rico based on the timing of conception.

BACKGROUND: Birth defects represent one of the main causes of infant mortality and morbidity around the world. OBJECTIVE: The purpose of this study is to identify seasonal changes in the incidence of various congenital anomalies in our population. METHODS: We identified all cases of open neural tube defects, cardiac anomalies, cleft lip and palate and gastroschisis of children born in Puerto Rico and reported to the Health's Department Birth Registry Program between January 1995 and December 2005. The conception dates were determined by estimation based on the reported last menstrual period. All deliveries during this same period were recorded and their conception dates estimated in the same manner. The data for each anomaly was separated into 4 groups for each year studied corresponding to the four seasons. The sample was stratified based on the type of anomaly detected and the season when conception took place. RESULTS: There is a seasonal pattern in the rate of conceptions in Puerto Rico with the highest incidence during the winter and lowest during the summer months. We detected a statistically significant increase in the incidence and relative risk during the summer months (using winter as a reference) of conceiving a child with open neural tube defects (1.03/1000, RR:1.33), cardiac anomalies (5.22/1000, RR:1.39), or cleft lip and palate (1.68/1000, RR:1.89). Gastroschisis did not show a statistically significant difference in the rate of conceptions, but there was a tendency towards a higher incidence during spring (0.39/1000, RR:1.67). CONCLUSIONS: The reported seasonal variation in the incidence of open neural tube defects, cardiac anomalies, and cleft lip and palate may be secondary to the effect of yet to be identified teratogens acting on the population at large, or, more likely, to changes in activity and dietary patterns of the population.

Fetal ultrasound biometry: normative charts for a Puerto Rican population.

PURPOSE: To evaluate fetal growth parameters throughout gestation in Puerto Rican women and compare them to other mixed U.S. populations. METHODS: Cross-sectional study of 548 patients who met inclusion criteria of Puerto Rican ancestry, no history of drug, alcohol or tobacco use, no identifiable fetal anomalies, normal amniotic fluid and certainty of last menstrual period. Standard sonographic biometric data (biparietal diameter, occipito-frontal diameter, head circumference, abdominal circumference, femur length and estimated fetal weight) was obtained for each gestational age between 13 and 38 weeks and the 10th, 50th, and 90th percentile determined for each one. Results were compared to those of other mixed U.S. populations. RESULTS: Biometric data on fetal growth throughout gestation among Puerto Ricans is presented. Comparison with other mixed populations did not show any significant differences in fetal biometric measurements throughout pregnancy. CONCLUSIONS: Different to other ethnic groups, Puerto Ricans show similar fetal growth patterns as those reported from mixed U.S. populations. This information validates the use of these reference values in the evaluation of fetuses in Puerto Rico.

Seasonal variation in the incidence of cleft lip and palate based on the age of conception.

BACKGROUND: The purpose of this study is to identify seasonal changes in the incidence of Cleft lip and Palate (CL/P) in our population. METHODS: All cases of isolated CL/P born in Puerto Rico from January 1998 through December 2002 were identified through the Puerto Rican birth defect registry. Conception dates were estimated based on the reported last menstrual period. All deliveries during this same period were recorded and their conception dates estimated in the same manner. The data was separated into 4 groups for each year studied corresponding approximately to the four seasons. RESULTS: 484 cases of CL/P were identified among 308,968 live births (incidence 1.57/1000 live births. The lowest incidence of CL/P was seen during fall and winter (1.24 and 1.38/1000 live births respectively) and the highest during spring and summer (1.77 and 1.97/1000 live births respectively) (p = 0.002). The seasons with the highest incidence correspond to the period when the least number of conceptions are occurring. Estimation of relative risks using winter as a reference point (relative risk of 1.0) showed a decrease in the risk of CL/P in fall to .89 (95th confidence interval 0.88 - 1.57), an increase in the risk to 1.28 (CI 1.16 - 2.03) during spring and 1.42 (CI 1.16 - 2.03) during summer. CONCLUSIONS: The reported seasonal variation in incidence may be secondary to the action of yet to be identified teratogens acting on the population at large, or more likely, changes in activity and diet patterns of the population.

Prenatal diagnosis of renal disease.

INTRODUCTION: The purpose of this study is to report the range of renal congenital anomalies identified by ultrasonography and to analyze the indications for the ultrasound study that lead to their diagnosis. MATERIALS AND METHODS: All cases of renal malformations diagnosed at our institution from June 2001 through May 2004 were evaluated retrospectively. The indications for sonographic evaluation were reviewed. Cases were divided into those referred for routine ultrasound screening and those referred with other indications. Results were expressed as percents of total. RESULTS: A total of 117 cases of renal congenital anomalies were identified, in 14 cases (11.9%), other congenital anomalies were also present. Hydronephrosis was the most common diagnosis detected in 64 cases (54.7%). There were 21 lethal renal anomalies identified (17.9%). Multicystic dysplastic kidneys were present in 21 cases (17.9%). Renal agenesis was identified in 15 cases (12.8%). Other detected anomalies were: bladder outlet obstruction 15 (12.8%), echogenic kidneys 13 (11.1%), ectopic ureteral implantation 2 (1.7%), renal cysts 1 (0.8%), pelvic kidney 3 (2.6%), double collecting system 1 (0.8%), and unilateral atrophic kidney 1 (0.8%). A total of 94 cases (80.3%) had no indications for sonographic evaluation other than routine screening. CONCLUSIONS: Relying on risk factors as indications for ultrasound studies will not detect the majority of congenital anomalies, especially those associated to the urogenital system, a group of conditions that may particularly benefit form prenatal detection.

Mitochondrial DNA error prophylaxis: assessing the causes of errors in the GEP'02-03 proficiency testing trial.

We report the results of the Spanish and Portuguese working group (GEP) of the International Society for Forensic Genetics (ISFG) Collaborative Exercise 2002-2003 on mitochondrial DNA (mtDNA) analysis. Six different samples were submitted to the participating laboratories: four blood stains (M1-M2-M3-M4), one mixture blood sample (M5), and two hair shaft fragments (M6). Most of the labs reported consensus results for the blood stains, slightly improving the results of previous collaborative exercises. Although hair shaft analysis is still carried out by a small number of laboratories, this analysis yielded a high rate of success. On the contrary, the analysis of the mixture blood stain (M5) yielded a lower rate of success; in spite of this, the whole results on M5 typing demonstrated the suitability of mtDNA analysis in mixture samples. We have found that edition errors are among the most common mistakes reported by the different labs. In addition, we have detected contamination events as well as other minor problems, i.e. lack of standarization in nomenclature for punctual and length heteroplasmies, and indels. In the present edition of the GEP-ISFG exercise we have paid special attention to the visual phylogenetic inspection for detecting common sequencing errors.