Comparison of the ABC and ACMG systems for variant classification.

The ABC and ACMG variant classification systems were compared by asking mainly European clinical laboratories to classify variants in 10 challenging cases using both systems, and to state if the variant in question would be reported as a relevant result or not as a measure of clinical utility. In contrast to the ABC system, the ACMG system was not made to guide variant reporting but to determine the likelihood of pathogenicity. Nevertheless, this comparison is justified since the ACMG class determines variant reporting in many laboratories. Forty-three laboratories participated in the survey. In seven cases, the classification system used did not influence the reporting likelihood when variants labeled as "maybe report" after ACMG-based classification were included. In three cases of population frequent but disease-associated variants, there was a difference in favor of reporting after ABC classification. A possible reason is that ABC step C (standard variant comments) allows a variant to be reported in one clinical setting but not another, e.g., based on Bayesian-based likelihood calculation of clinical relevance. Finally, the selection of ACMG criteria was compared between 36 laboratories. When excluding criteria used by less than four laboratories (<10%), the average concordance rate was 46%. Taken together, ABC-based classification is more clear-cut than ACMG-based classification since molecular and clinical information is handled separately, and variant reporting can be adapted to the clinical question and phenotype. Furthermore, variants do not get a clinically inappropriate label, like pathogenic when not pathogenic in a clinical context, or variant of unknown significance when the significance is known.

Clinical relevance of the TECTA c.6183G>T variant identified in a family with autosomal dominant hearing loss: a case report.

Missense variants in the α-tectorin gene (TECTA) cause autosomal dominant (DFNA8/A12) non-syndromic hearing loss (ADNSHL) and account for a considerable number of ADNSHL cases. According to genotype-phenotype correlation studies, missense variants in the zona pellucida (ZP) domain of α-tectorin predominantly cause mid-frequency HL. Here, we report on clinical exome sequencing results in a large family with early-onset, sensorineural, moderate-to-severe mid-frequency HL. We identified one heterozygous c.6183G>T variant near the ZP domain of TECTA segregating in five family members. This variant was previously reported as a variant of uncertain significance in a family with ADNSHL. On the basis of specific segregation in the currently studied family and the general guidelines of the American College of Medical Genetics and Genomics, we argue that the TECTA c.6183G>T variant should be considered a likely pathogenic cause of ADNSHL. This report adds to the knowledge on the rare c.6183G>T missense variant, which affects the immediate vicinity of the ZP domain in TECTA. Our findings highlight the importance of clinical evaluation in patients with familial HL and of studying family segregation when assessing the pathogenicity of a variant.

The first case report of distal 16p12.1p11.2 trisomy and proximal 16p11.2 tetrasomy inherited from both parents.

Recurrent copy number variants in the chromosomal region 16p11.2 are among the most frequent genetic causes of neurodevelopmental disorders. The increasing prevalence of brain structural anomalies is also associated with 16p11.2 deletions and duplications. We report on a four-year-old boy with microcephaly, trigonocephaly, and dysmorphic features. The patient also exhibited motor delay and autism spectrum disorder. Microarray analysis showed a single-copy gain of a 1.187 kb segment in the 16p12.1p11.2 region and a two-copy gain of a 525 kb segment in the 16p11.2 region. Parental analysis revealed a 1.7 Mb duplication at the 16p12.1p11.2 (BP1-BP5 region) in the father and a 525 kb duplication in the 16p11.2 region (BP4-BP5) in the mother. The patient inherited the entire abnormality from each parent and, as a result, presented with partial trisomy of the 16p12.1p11.2 region and partial tetrasomy of the 16p11.2 region. The MLPA P343 Autism-1 Probemix was used to verify the copy number gains in the 16p11.2 region detected by chromosomal microarray analysis. Double duplications are very rare chromosomal rearrangements. The phenotype for distal 16p12.1p11.2 trisomy (BP1-BP3) and proximal 16p11.2 (BP4-BP5) tetrasomy is unknown. To our knowledge, this is the first patient described in the literature who inherited 16p11.2 duplications from both parents.

Trends in the treatment of undescended testes: a pediatric tertiary care center experience from Croatia.

Objective: Undescended testes (UDT) is the most common anomaly of the male genitourinary tract. The guidelines suggest that orchidopexy in congenitally UDT should be performed between 6 months and 18 months of age, while in acquired UDT, orchidopexy should be performed before puberty. Delay in treatment increases the risk of cancer and infertility. The main aim of this study was to determine whether we meet international standards in the treatment of UDT. Methods: The present study included all boys who underwent orchidopexy either due to congenital or acquired UDT in 2019 (from January 1 to December 31). For each group, laterality, location, associated anomalies, premature birth and in how many cases ultrasound was applied were determined. Additionally, for each group, the types of surgery, the number of necessary reoperations, and in how many cases atrophy occurred were determined. Finally, ages of referral, of clinical examination, and of orchidopexy were determined. Results: During this period, 198 patients with 263 UDT underwent orchidopexy. The median time of orchidopexy for the congenital group was 30 months, while that for the acquired group was 99 months. In the congenital group up to 18 months of age, orchidopexy was performed in 16 (16%) boys, while in the acquired group up to 13 years of age, orchidopexy was performed in 95 (96.94%) boys. Conclusion: Given the well-known risks of late treatment of UDT, orchidopexy needs to be performed much earlier, especially in the congenital group.

Beckwith Wiedemann syndrome: A population-based study on prevalence, prenatal diagnosis, associated anomalies and survival in Europe.

Beckwith Wiedemann syndrome is a complex developmental disorder characterized by somatic overgrowth, macroglossia, abdominal wall defects, neonatal hypoglycemia, and predisposition to embryonal tumors. We present epidemiological and clinical aspects of patients with Beckwith Wiedemann syndrome diagnosed prenatally or in the early years of life, using data from EUROCAT (European Surveillance of Congenital Anomalies) registries. The study population consisted of 371 cases identified between January 1990 and December 2015 in 34 registries from 16 European countries. There were 15 (4.0%) terminations of pregnancy after prenatal detection of severe anomaly/anomalies, 10 fetal deaths (2.7%), and 346 (93.3%) live-births. Twelve (3.6%) of the 330 live-births with available information on survival died in the first week of life, of those eleven (91.6%) were preterm. First-year survival rate was 90.9%. Prematurity was present in 40.6% of males and 33.9% of females. Macrosomia was found in 49.2% and 43.3% of preterm males and females, respectively. Of term newborns, 41.1% of males and 24% of females were macrosomic. Out of 353 cases with known time of diagnosis, 39.9% were suspected prenatally, 36.3% at birth, 7.6% were diagnosed in the first week of life, and 16.2% in the first year of life. The mean gestational age at prenatal diagnosis by obstetric ultrasound was 19.8 ±â€¯6.2 (11-39) gestational weeks. The mean prenatal diagnosis of cases where parents opted for termination of pregnancy was 15.3 ±â€¯2.4 (11-22) gestational weeks, and the mean gestational age at termination was 19.3 ±â€¯4.1 (13-26) gestational weeks. The prenatal detection rate was 64.1% (141/220) with no significant change over time. There were 12.7% of familial cases. The study confirmed the association of assisted reproductive technologies with Beckwith Wiedemann syndrome, as 7.2% (13/181) of patients were conceived by one of the methods of assisted reproductive technologies, which was three times higher compared to the general population of the countries included in the study. Twin pregnancies of undetermined zygosity were recorded in 5.7% (21/365) cases, and were on average three to four times more common than in European countries that participated in the study. The estimated mean prevalence of classical Beckwith Wiedemann syndrome in Europe was 3.8 per 100,000 births or 1:26,000 births.

Chromosomal microarray in clinical diagnosis: a study of 337 patients with congenital anomalies and developmental delays or intellectual disability.

AIM: To determine the diagnostic yield and criteria that could help to classify and interpret the copy number variations (CNVs) detected by chromosomal microarray (CMA) technique in patients with congenital and developmental abnormalities including dysmorphia, developmental delay (DD) or intellectual disability (ID), autism spectrum disorders (ASD) and congenital anomalies (CA). METHOD: CMA analysis was performed in 337 patients with DD/ID with or without dysmorphism, ASD, and/or CA. In 30 of 337 patients, chromosomal imbalances had previously been detected by classical cytogenetic and molecular cytogenetic methods. RESULTS: In 73 of 337 patients, clinically relevant variants were detected and better characterized. Most of them were >1 Mb. Variants of unknown clinical significance (VOUS) were discovered in 35 patients. The most common VOUS size category was <300 kb (40.5%). Deletions and de novo imbalances were more frequent in pathogenic CNV than in VOUS category. CMA had a high diagnostic yield of 43/307, excluding patients previously detected by other methods. CONCLUSION: CMA was valuable in establishing the diagnosis in a high proportion of patients. Criteria for classification and interpretation of CNVs include CNV size and type, mode of inheritance, and genotype-phenotype correlation. Agilent ISCA v2 Human Genome 8x60 K oligonucleotide microarray format proved to be reasonable resolution for clinical use, particularly in the regions that are recommended by the International Standard Cytogenomic Array (ISCA) Consortium and associated with well-established syndromes.

Molecular genetic analysis in 93 patients and 193 family members with classical congenital adrenal hyperplasia due to 21-hydroxylase deficiency in Croatia.

Congenital adrenal hyperplasia owing to 21-hydroxylase deficiency is caused by mutation in the CYP21A2 gene. The frequency and spectrum of CYP21A2 mutations and genotype-phenotype correlations among different populations are variable. Aim of this study was to define mutation frequency and spectrum of CYP21A2 gene mutations in patients with classical 21-hydroxylase deficiency (21OHD) and their family members in Croatia and study genotype-phenotype correlation. Clinical features and mutations of CYP21A2 gene in 93 unrelated 21OHD patients and 193 family members were examined. In this cohort, 66 patients were affected with salt wasting (SW) form, and 27 were affected with simple virilizing (SV) form of the disease. Mutations were identified in both alleles (67% compound heterozygous and 33% homozygous) in 91 of 93 patients. Deletions and conversions were found in 18.8% and point mutations in 79.6% alleles. Mutations in 3 alleles (1.6%) remained unidentified (in one patient we found only one, while in other no mutations were found at all). The most common point mutations were Intron 2 splice mutation IVS2-13 A/C>G (35.5%) and p.R357W (16.7%). Genotypes were categorized into Groups 0, A, B and C according to the extent of enzyme impairment. Genotype-phenotype concordance was 100%, 85% and 75% for Groups 0, A and B, respectively. Since only classical 21OHD patients were studied, Group C comprised solely p.P31L mutation and had 73% patients with SV and 27% with SW phenotype. Intrafamilial phenotypic variability was found in two families. CYP21A2 genetic analysis in 193 family members showed that 126 parents were heterozygous carriers, 3 were newly discovered patients, 2 fathers were not biological parents, and mutations were not detected in 3. Among 59 siblings, 32 were heterozygous carriers, 15 carried normal alleles, and 12 were patients (4 newly diagnosed). Genotype-phenotype divergence observed in this study suggests caution in preconceptional counseling and prenatal diagnosis of CAH. High frequency of p.R357W mutation was found in Croatian patients with classical 21-OHD. Genotyping of family members discovered new patients and thus avoided pitfalls in genetic counseling when the parents were found to be affected.

Improved detection of deletions and duplications in the DMD gene using the multiplex ligation-dependent probe amplification (MLPA) method.

The multiplex ligation-dependent probe amplification (MLPA) assay is the most powerful tool in screening for deletions and duplications in the dystrophin gene in patients with Duchenne and Becker muscular dystrophy (DMD/BMD). The efficacy of the assay was validated by testing 20 unrelated male patients with DMD/BMD who had already been screened by multiplex PCR (mPCR). We detected two duplications that had been missed by mPCR. In one DMD patient showing an ambiguous MLPA result, a novel mutation (c.3808_3809insG) was identified. MLPA improved the mutation detection rate of mPCR by 15 %. The results of our study (1) confirmed MLPA to be the method of choice for detecting DMD gene rearrangements in DMD/BMD patients, (2) showed that ambiguous MLPA amplification products should be verified by other methods, and (3) indicated that the MLPA method could be used in screening even for small mutations located in the probe-binding regions.

Hypochondroplasia due to FGFR3 gene mutation (N540K) and mosaic form of Down syndrome in the same patient.

The simultaneous presence of Down syndrome and achondroplasia has rarely been reported in the literature, and our search revealed only six patients with such an association. We are reporting the first case of a patient with Down syndrome and hypochondroplasia. In this patient, Down syndrome was clinically recognised and confirmed by the cytogenetic finding of mosaic karyotype (47,XX,+21/46,XX) shortly after birth. She was subsequently diagnosed with hypochondroplasia at the age of 6 years when disproportional short stature, stocky habitus and macrocephaly were observed. These phenotypic findings were later confirmed by the presence of fibroblast growth factor receptor 3 (FGFR3) gene mutation N540K. The overlapping common clinical features of Down syndrome and hypochondroplasia resulted in delayed diagnosis of hypochondroplasia in our patient and the associated deleterious effect on her linear growth. Her final height is 126.5 cm, which is -3.76 standard deviations (SD) lower than the median height in patients with Down syndrome, and is under the lower borderline of the adult height range for women with hypochondroplasia.

GJB2 mutations in patients with nonsyndromic hearing loss from Croatia.

The aim of the study was to determine (1) the frequency and type of mutations in the coding region of the GJB2 gene (sequencing), (2) the frequency of splice site mutation IVS1 + 1G > A in the GJB2 gene (multiplex ligation-dependent probe amplification analysis), (3) possible copy number changes in the GJB2, GJB3, GJB6, and WFS1 genes (multiplex ligation-dependent probe amplification analysis), and (4) the frequency of del(GJB6-D13S1830) in the GJB6 gene in 58 unrelated patients with nonsyndromic hearing loss from Croatia. About 44.8% of our patients presented with mutation in the GJB2 gene. We identified seven sequence variations. Six of them had previously been reported as disease related (35delG, W24X, V37I, L90P, 313del14, and IVS1 + 1G > A), and we report here for the first time one novel variant, -24A > C. We detected the greatest frequency of 35delG allele compared to the other alleles (35.3%). Allelic frequencies of other common mutations accounted for 2.6-0.9% of analyzed chromosomes. Neither GJB6 deletion nor copy number changes in the GJB2, GJB3, GJB6, and WFS1 genes were found. The 35delG/35delG genotype was associated with severe to profound hearing loss in 94% of 35delG homozygotes. High mutation rate (44%) indicates that testing of the GJB2 gene will clarify the genetic cause in almost half of the cases of recessive nonsyndromic hearing loss in Croatia.

Prevalence of the 35delG mutation in the GJB2 gene of patients with nonsyndromic hearing loss from Croatia.

The aim of this study was to investigate the allelic frequency of 35delG mutation in patients with recessive, nonsyndromic hearing loss (NSHL) compared to normal hearing individuals in the Croatian population. For this purpose, we analyzed 27 unrelated individuals with nonsyndromic hearing loss and 342 healthy individuals. The method we used is based on the principle of polymerase chain reaction (PCR)-mediated, site-directed mutagenesis, followed by a BsiYI digestion. Among patients with NSHL, the 35delG mutation was found on 51.85% alleles. Carrier frequency among healthy control individuals was 1 in 68.4 (1.5%). The patients, found to be wild-type, either in heterozygous or homozygous form, were further tested by direct sequencing. Among them, two different mutations were observed, W24X and 313del14. Relatively high prevalence of 35delG mutation among patients with NSHL indicate that it is an important cause of NSHL in Croatia. Early diagnosis by identification of the 35delG mutation would greatly improve genetic counseling, as well as treatment and management of deafness in Croatia.