Sanger sequencing is no longer always necessary based on a single-center validation of 1109 NGS variants in 825 clinical exomes.

Despite the improved accuracy of next-generation sequencing (NGS), it is widely accepted that variants need to be validated using Sanger sequencing before reporting. Validation of all NGS variants considerably increases the turnaround time and costs of clinical diagnosis. We comprehensively assessed this need in 1109 variants from 825 clinical exomes, the largest sample set to date assessed using Illumina chemistry reported. With a concordance of 100%, we conclude that Sanger sequencing can be very useful as an internal quality control, but not so much as a verification method for high-quality single-nucleotide and small insertion/deletions variants. Laboratories might validate and establish their own thresholds before discontinuing Sanger confirmation studies. We also expand and validate 23 copy number variations detected by exome sequencing in 20 samples, observing a concordance of 95.65% (22/23).

[Characteristics of neonates with and without a single umbilical artery. Analysis of two consecutive series of neonates with and without congenital defects]. / Características de los neonatos con y sin arteria umbilical única. Análisis de dos series consecutivas de recién nacidos con y sin defectos congénitos.

BACKGROUND AND OBJECTIVE: The implications of the presence of a single umbilical artery (SUA) are unknown. Although most articles are based on selected samples, they suggest a relationship between SUA and malformations. Consequently, prenatal detection of SUA causes concern, since there are no definitive guidelines that can be followed after identification of this abnormality. The objective of this study was to comparatively analyze SUA in two series of consecutive births, with and without congenital defects. PATIENTS AND METHODS: A total of 19,909 cases and 19,148 controls from the Registry of the Spanish Collaborative Study on Congenital Malformations were studied. The variables analyzed were sex, birth weight, length, occipito-frontal circumference, gestational age, prematurity, delivery by caesarean section, umbilical cord length, placental weight, survival at 72 hours, primiparity, oligohydramnios, and polyhydramnios. Calculations included relative frequency, odds ratios (OR) and 95 % confidence intervals, the chi-square test, Fisher's p-value, and Student's t-test. RESULTS: SUA was found in 2.29 % of cases and in 1.03 % of controls (p = 0.0000001). These figures showed secular variation due to improvements in prenatal diagnosis and interruption of some pregnancies. When cases with and without SUA were compared, those with SUA had lower values of somatometry at birth, umbilical cord length and gestational age and had a higher risk for oligohydramnios, polyhydramnios, caesarean section, and death in the first 72 hours. Among controls, the only differences were a shorter umbilical cord and a higher frequency of oligohydramnios among infants with SUA. CONCLUSIONS: The results suggest that certain malformations associated with SUA could cause some of the differences among cases. Shortening of the umbilical cord and oligohydramnios could be related to SUA, as these abnormalities were found in both cases and controls. Comparison of cases and controls suggests that the etiopathogenesis of SUA could differ in the two groups.

Epidemiological evidence that maternal diabetes does not appear to increase the risk for Down syndrome.

In 1997, Narchi and Kulaylat, studying the incidence of Down syndrome in infants of gestational diabetic mothers, concluded that maternal diabetes increases the risk for Down syndrome, but failed to control the maternal age in their analysis. Using data from the Spanish Collaborative Study of Congenital Malformations (ECEMC), we analyzed the relationship between Down syndrome and maternal diabetes mellitus, and maternal gestational diabetes, controlling the maternal age through the pair-matching analysis, stratifying by maternal age and logistic regression analysis. The analyses show that maternal age is related either to Down syndrome as well as to both types of maternal diabetes. Thus, the overall analysis could be confounded by maternal age. Once we controlled the maternal age, the risk of maternal diabetes mellitus for Down syndrome is: odds ratio (OR) = 0.92 (0.41-2.07); P = 0.83. Controlling maternal age in gestational diabetes, the risk is OR = 1.18 (0.61-2.35); P > 0.70. Based on our results, we conclude that Down syndrome is related to maternal age, but does not seem to be related to any type of maternal diabetes.

Body stalk defects, body wall defects, amniotic bands with and without body wall defects, and gastroschisis: comparative epidemiology.

The presence of body wall defects with "evisceration" of thoracic and/or abdominal organs associated with other congenital anomalies, with or without limb deficiencies, is considered to be the body wall complex (BWC). The BWC is different from gastroschisis, which is usually a small body wall defect lateral to the umbilical cord that is not covered by any membrane and, in most of the cases, is an isolated defect. For the present analysis we separated the BWC group into three subgroups. One group was that of body stalk anomalies characterized by severe defects of the abdominal wall with absence of, or very small, umbilical cord, or this is continuing with the placenta. The second group was made up of those infants with body wall defects without amniotic bands, and the third group was of those children with body wall defects produced by amniotic bands. We considered two additional groups in the analysis, one was of infants with gastroschisis and the other those infants with amniotic bands without body wall affectation. We also included the control group (nonmalformed infants) for comparisons. From the results of our epidemiological study, we can conclude that amniotic bands with body wall affectation and amniotic bands without body wall defects are two different entities. The results also suggest that the characteristics of infants with amniotic bands with body wall defects are more similar to the group of infants with body stalk anomalies. This may indicate that the former group is produced during the very early gestation.

Anal atresia, vertebral, genital, and urinary tract anomalies: a primary polytopic developmental field defect identified through an epidemiological analysis of associations.

Anal atresia (AA) is observed per se or as part of different Mendelian or chromosomal syndromes, and as part of the VACTERL primary developmental field, CHARGE association, cloacal extrophy, in a mitochondrial cytopathy, and other multiple congenital anomaly patterns. There are only a few studies on the defects associated with AA, and in all of them it was observed that genitourinary defects are most frequent in infants with AA. Here we present the analysis of 28,410 malformed infants to study the frequency of 11 selected congenital defects in infants with AA in relation to their frequency in infants with multiple congenital anomaly patterns without AA. We conclude that the association of AA + spine defects + renal/urinary tract defects + genital defects constitutes a group of defects that tends to be present together in the same child because they are pathogenetically related, and since they are of blastogenetic origin they constitute a primary polytopic developmental field defect.

Epidemiological analysis of the schisis association in the Spanish registry of congenital malformations.

Since its description by Czeizel [1981: Am J Med Genet 10:25-35], there has been general acceptance of the schisis association as a distinct entity although, to the best of our knowledge, no other epidemiological study has confirmed its existence. Here we present an epidemiologic study on schisis defects and their associations with each other in children with and without blastogenetic defects. This study demonstrates that most cases represent the dysmorphogenetic response of the primary developmental field.

Exstrophy of the cloaca and exstrophy of the bladder: two different expressions of a primary developmental field defect.

Exstrophy of the bladder (EB) and exstrophy of the cloaca (EC) are generally recognizable as distinct clinical entities. In patients with EB, the posterior bladder wall is exposed through a midline defect of the abdomen. The umbilicus is inferiorly displaced and located close to the superior margin of the exstrophic bladder. Genital abnormalities are common in boys and girls who may present epispadias and a small, split phallus or a split clitoris, a bifid uterus, and a duplicate or exstrophic vagina. In contrast to classic EB, EC is commonly associated with omphalocele, spinal defects, and incompletely formed external genitalia and is always associated with imperforate anus. Some authors state that EC and EB constitute two distinct disorders, but others consider them part of a "continuum," representing different levels of severity within the same spectrum. The use of the acronym OEIS to refer to the combination of omphalocele, exstrophy, imperforate anus, and spinal defects, in our opinion, has not helped to clarify the clinical definition, pathogenesis, or cause of this multiple congenital anomaly (MCA) pattern, mostly because the term makes no distinction between EC or EB. Here we present the epidemiological analysis of a group of characteristics in infants with EC and infants with EB to determine if they constitute two different entities. We also analyze if the different combinations of omphalocele, imperforate anus, and spinal defects are more frequent in infants with EC than in infants with MCA patterns other than EC and EB. The prevalence in our data for EC was 1:200,233 live births and 1:35,597 for EB. The clinical analysis indicated that the study defects (omphalocele, spine defects, spina bifida, and imperforate anus) tend to occur together in the same child with a higher frequency if the child has the EC defect than in infants with MCA patterns that did not include EC or EB. Our findings of low birth weight, twinning, single umbilical artery, and preferentially associated malformations suggest that EC is the result of damage occurring very early in development and that EC and EB are two different expressions of a primary polytopic developmental field defect.

Epidemiological analysis of outcomes of pregnancy in gestational diabetic mothers.

The association between maternal diabetes mellitus and congenital defects has been well documented. However, few data exist on the potential teratogenic effect of gestational diabetes (GD). We analyzed 19,577 consecutive infants with malformations of unknown cause and compared the offspring of mothers with GD with those of nondiabetic mothers. The children with each of 20 types of selected anomalies among the two groups were used to calculate the odds ratio (OR). Because we used as a reference group for each congenital defect the rest of malformed infants, the value of the OR gives us the specificity between the association of GD and each congenital defect. Our analysis strongly supports the suggestion that GD is a significant risk for holoprosencephaly, upper/lower spine/rib, and renal and urinary system anomalies. GD is a heterogeneous disorder, which includes previously unrecognized and newly diagnosed nongestational diabetes mellitus (DM). Thus, it is possible that the teratogenic effect is related to latent DM. However, because it is not possible at this time to differentiate between these situations, pregnancies complicated by GD should be considered at risk for congenital anomalies. Prenatal ultrasound examination should be aimed particularly at the detection of abnormalities of the central nervous system, the renal and urinary system, and the spine/rib developmental field.

Epidemiological analysis of multi-site closure failure of neural tube in humans.

Van Allen et al. [Am J Med Genet 47:723-743, 1993] proposed that there is multi-site initiation of neural tube closure in humans, and that neural tube defects (NTD) represent the failure of one or more of 5 closure sites. We have studied from an epidemiologic perspective 774 liveborn infants with NTD by site of lesion following the multi-site classification proposed by Van Allen et al. [1993]. As predicted by these authors, we could classify all the cases with NTD by the multisite closure model. We have also estimated the prevalence of each failure closure site. This analysis indicates that not all the sites are affected with similar frequency.

Prenatal exposure to valproic acid during pregnancy and limb deficiencies: a case-control study.

We conducted a case-control study using data from the Spanish Collaborative Study of Congenital Malformations (ECEMC) on the relationship between prenatal exposure to valproic acid (VPA) and the presence of limb deficiencies in newborn infants. Among a total of 22,294 consecutive malformed infants (once we excluded genetic syndromes) and 21,937 control infants with specified data on antiepileptic drugs during gestation, 57 malformed infants and 10 control infants were exposed to VPA during the first trimester of pregnancy. Of the total of malformed infants exposed to VPA, 36.8% (21/57) presented with congenital limb defects of different types (including overlapping digits, talipes, clubfoot, clinodactyly, arachnodactyly, hip dislocation, pre- and postaxial polydactyly, etc.), three of them having limb deficiencies. The result of the case-control analysis shows a risk for limb deficiencies of odds ratio = 6.17 [confidence interval (CI) 1.28-29.66, P = 0.023], after controlling for potential confounder factors. If we consider that in our population the prevalence at birth of this type of defect is 6.88 per 10,000 livebirths (95% CI 6.43-7.36) we can estimate that the risk for women treated with VPA of having a baby with limb deficiencies would be around 0.42%. The limb deficiencies in the three patients exposed to VPA were the following: the first case was a newborn infant with hypoplasia of the left hand, the second patient was a newborn infant with unilateral forearm defect and hypoplastic first metacarpal bone in the left hand, and the third patient presented with short hands with hypoplastic first metacarpal bone, absent and hypoplastic phalanges, retrognathia, facial asymmetry, hypospadias, teleangiectatic angioma in skull, and hypotonia.

Primary midline developmental field. II. Clinical/epidemiological analysis of alteration of laterality (normal body symmetry and asymmetry).

Lubinsky [Am J Med Genet 3:23-28, 1987] has suggested that the properties of the midline involve early determinative informational processes and are related to the midline's position and definition of the body's plane of symmetry. Opitz [Am J Med Genet 21:175-176, 1985, BD: OAS XXIX(1):3-37 1993] has pointed out that the laterality sequences represent a midline developmental field complex. Thus, bilateral left-sidedness (with asplenia) and bilateral right-sidedness (with asplenia) have been considered laterality sequences or syndromes if cause is known. Using the malformed infants registered by the Spanish Collaborative Study of Congenital Malformations (ECEMC), we performed a clinical/epidemiological analysis of the relationship between midline defects and alteration of normal body asymmetry and symmetry. The results support the assumption that both conditions could be consequence of disturbances in the midline primary developmental field.

Value of clinical analysis in epidemiological research: the Spanish registry experience.

Using data from the Spanish Collaborative Study of Congenital Malformations (ECEMC), a hospital-based, case-control study and surveillance program, we investigated the potential value of registry systems in the identification of causes of congenital defects when their methodology includes (1) detailed reporting and coding of all anomalies present in each child, whether major or minor, (2) clinical analysis and coding of the global pattern of anomalies present in each infant, and (3) classification of all children studied according to their clinical presentation. These approaches provide great specificity and flexibility in the retrieval and analysis of data. Not only do they permit the study of specific anomalies, but also the analysis of children with MCA patterns, as well as the study of the relationship of specific defects with the rest of the anomalies present in a child. To illustrate this point, we present general data on 15,307 malformed children and more specific information on 153 cases of anal atresia/stenosis identified among the 753,410 live-births surveyed by the ECEMC between April 1976 and September 1989.

Prevalence of dominant mutations in Spain: effect of changes in maternal age distribution.

We studied the birth prevalence of autosomal dominant mutations in Spain and estimated how a decrease in maternal age distribution may lead to reduction in dominant mutations. The data were collected by the Estudio Colaborativo Español de Malformaciones Congénitas from April, 1976, to December, 1985. Among 553,270 liveborn infants monitored during the period, 66 infants with autosomal dominant conditions were identified. These included Apert, Crouzon, Hay-Wells, Treacher-Collins, Robinow, Stickler, Adams-Oliver, and the blepharophimosis syndromes, achondroplasia, cleidocranial dysostosis, and thanatophoric dysplasia. The overall rate of autosomal dominant conditions was 1.2 per 10,000 liveborn infants. Thirteen (20%) had an affected relative, and 52 (79%) had a negative family history. One case was excluded because of insufficient family data. The rate of autosomal dominant mutations was 0.9 per 10,000 liveborn infants, or 47 per 1 million gametes. A reduction in the maternal age distribution of mothers age 35 years and older from the current 10.8% to 4.9%, as in Atlanta, Georgia, would reduce the rate of Down syndrome in Spain by 33% and through a change in parternal age distribution may lead to a reduction in dominant mutations of about 9.6%. This suggests that a public health campaign to reduce older maternal age distribution in Spain may also lead to a reduction in dominant mutations and emphasizes the potential that a direct campaign for fathers to complete their families before age 35 years may have a small, but measurable, effect in the primary prevention of dominant mutations.

High maternal fever during gestation and severe congenital limb disruptions.

Hyperthermia is defined as a temperature of at least 1.5 degrees C over the normal core body temperature. It is a proven teratogen in animals and in humans. The type of defects induced by hyperthermia in experimental animals are: anencephaly/exencephaly, encephalocele, microphthalmia, arthrogryposis, abdominal wall defects, limb deficiencies, embryonic death, and resorption. In humans it has been observed that infants prenatally exposed to hyperthermia presented with spina bifida, encephalocele, microphthalmia, micrognathia, external ear anomalies, cardiac defects, hypospadias, gastrointestinal defects, cleft lip and/or cleft palate, abdominal wall defects, diaphragmatic hernia, Hirschsprung disease, Möbius syndrome, oromandibular-limb hypogenesis spectrum, and spontaneous abortions. We describe an additional case with severe limb deficiencies whose mother had fever over 39 degrees C for 2 days in the second and in the fourth month of amenorrhoea. We conclude that, based on the degree of development of the humeri and the femora and the type of limb deficiencies, this case presents a disruption that most probably occurred in the fourth month of gestation.

The outcome of pregnancy in 689 women exposed to therapeutic doses of antidepressants. A collaborative study of the European Network of Teratology Information Services (ENTIS).

The European Network of the Teratology Information Services (ENTIS) has collected and evaluated data on 689 pregnancies in which exposure to tricyclic and nontricyclic antidepressants occurred. Data were collected prospectively from the time of in utero exposure and all the cases were followed up to the first few weeks of postnatal life using standardized procedures. In most cases, no longer term follow-up data were available. Approximately two-thirds of the mothers were on multidrug therapy, and of those, half took a benzodiazepine. About 95% of the patients were exposed during the first trimester. The most striking feature of the pregnancy outcomes is that 97% of live-born babies were morphologically normal. The incidence of spontaneous abortion and late fetal/neonatal deaths were within the normal range. Fourteen live-born babies and one fetus had either major or minor malformations, and six had minor anomalies. However, there was no increase in either a particular type of malformation or a specific pattern of defects. Another 31 infants without malformations had neonatal problems; these were usually associated with chronic multidrug therapy, especially near term. Elective termination of pregnancy occurred more frequently in the multidrug groups (86 out of 488) than in the monotherapy groups (20 out of 201), but data concerning the condition of the fetus are not available in the majority of the cases. Overall, no causal relationship could be established between in utero exposure to antidepressants and adverse pregnancy outcome.

Periconceptional exposure to contraceptive pills and risk for Down syndrome.

OBJECTIVE: There are some studies which analyzed the relationship between prenatal exposure to oral contraceptives (OCs) and Down syndrome, with conflicting results even in women using OCs and conceiving at different intervals after discontinuing the use of contraceptive pills. We analyzed the risk for Down syndrome in infants of women who become pregnant while taking OC. STUDY DESIGN: We used the data from the Spanish Collaborative Study of Congenital Malformations (ECEMC). The ECEMC is a case-control study and surveillance system. For each malformed infant (case), the next non-malformed infant of the same sex born in the same hospital is selected as a control subject, from whom the collaborating physicians collected the same data as for the malformed infant. For the present study, we used two different approaches. First, the pair-matching analysis. Second, a case-control using the rest of the total of 17,183 controls from the ECEMC database with specified data on maternal use of OCs and maternal age. To control for maternal age, we used a logistic regression analysis. RESULTS: The results show an increased risk of 2.8-fold for infants with Down syndrome in women younger than 35 years of age if the mother became pregnant while she was taking OCs. We did not observe this result for women older than 34 years of age. CONCLUSION: Our results showed that the risk for Down syndrome in infants born to mothers with less than 35 years of age (as a group) who became pregnant while taking OCs is near the risk for Down syndrome of mothers with more than 34 years of age, women who are candidates for prenatal diagnosis. Thus, based on our results, one may consider the possibility of offering prenatal diagnosis for Down syndrome to young women who became pregnant while taking OCs.

Maternal and fetal factors related to abnormal amniotic fluid.

OBJECTIVE: The objective of this study was to identify maternal and infant characteristics related to alteration of amniotic fluid volume at birth. STUDY DESIGN: A series of 27,145 consecutive malformed newborn infants from the Spanish Collaborative Study of Congenital Malformations (ECEMC) was analyzed. From this total, 3.01% were found to have oligohydramnios and 3.69% were found to have polyhydramnios. RESULTS: As expected, renal/urinary tract and lung defects were associated with oligohydramnios, whereas esophageal and intestinal atresias, neural tube defects, and other central nervous system malformations were associated with polyhydramnios. In addition, other defects such as cardiovascular anomalies, hydrocephaly, and microcephaly were also related to abnormalities of amniotic fluid volume. After excluding the defects whose association to oligo- or polyhydramnios is well recognized, we compared the frequency of different variables among them and with infants with a normal volume of amniotic fluid. In comparison with infants with normal amniotic fluid volume, the groups with oligo- and polyhydramnios had lower birth weight, shorter gestational age and umbilical cord, higher parental ages, and a greater frequency of spontaneous abortions. The differences were more marked for weight in newborn infants with oligohydramnios, and for gestational age, umbilical cord length, number of previous pregnancies, and spontaneous abortions in polyhydramnios cases. Placental weight was lower in oligohydramnios cases than in infants with normal amniotic fluid, and higher in polyhydramnios cases. Parental consanguinity and twinning were more frequent in polyhydramnios. Maternal morbidity was higher in both groups with abnormal amniotic fluid volume, especially for acute diseases such as hypertension, diabetes mellitus, and gestational diabetes. Chromosomal aberrations were more frequent in the oligo- and polyhydramnios groups than in cases with a normal volume of amniotic fluid, which supports the suggestion of performing prenatal cytogenetic analysis in any pregnancy complicated by an abnormal volume of amniotic fluid. CONCLUSION: The fact that all of these results are similar in the control group of healthy infants suggests that at least some of the variables associated with abnormal amniotic volume could be considered as causal factors altering the production of fluid.

Pregnancy outcome after prenatal quinolone exposure. Evaluation of a case registry of the European Network of Teratology Information Services (ENTIS).

OBJECTIVE: To study potential teratogenic effects of quinolone exposure during pregnancy. STUDY DESIGN: Prospective follow-up study. Subjects are pregnant women who contacted a teratology information center for risk information on quinolone treatment. A total of 549 pregnancies was collected by the European Network of Teratology Information Services between 1986 and 1994. In addition 116 prospectively documented pregnancies and 25 retrospective case reports on malformed children from other databases were analyzed. RESULTS: The malformation rate among the live-born babies in the prospective ENTIS cohort was approximately 4.8%. No specific patterns of congenital abnormalities were found. The results do not suggest an elevated risk for spontaneous abortion, prematurity, intrauterine growth retardation and postnatal disorders. CONCLUSION: The present study does not reveal any clear adverse reactions (fetal and neonatal toxicity, including birth defects) due to the in utero exposure to quinolones. Hence, termination of pregnancy because of such exposure is not indicated. However, considering the limitations of this study and the fact that diseases urgently requiring quinolone treatment are rare, it appears advisable to prefer penicillin, cephalosporins and erythromycin as antibiotics of choice.