Genetic counseling for cystic fibrosis: A basic model with new challenges.

While the goals of genetic counseling for cystic fibrosis - delivering relevant information on the risk of recurrence and nondirectional support of couples at risk in their reproductive choices - have not changed fundamentally, the practice has evolved considerably in the last decade, growing more complex to face new challenges but also proving more effective. Many factors have contributed to this evolution: technical progress in the exploration of the genome (new generation sequencing) and in reproductive medicine, but also societal developments promoting access to genetic information and the professionalization of genetic counselors in France. The prospect of expanded pre-conception screening of at-risk couples makes genetic counselors major actors not only in medical care centers, but also in modern society by contributing to genetic education among citizens. © 2020 French Society of Pediatrics. Published by Elsevier Masson SAS. All rights reserved.

Performance of semiconductor sequencing platform for non-invasive prenatal genetic screening for fetal aneuploidy: results from a multicenter prospective cohort study in a clinical setting.

OBJECTIVE: To validate and evaluate the performance metrics of the high-throughput semiconductor sequencing platform, Ion Proton®, in non-invasive prenatal genetic screening (NIPS) for common fetal aneuploidies in a clinical setting. METHODS: This prospective cohort study included 2505 pregnant women from eight academic genetics laboratories (695 high risk for trisomy 21 (risk ≥ 1/250) pregnancies in a validation study, and 1810 such pregnancies, without ultrasound anomalies, in a real-life NIPS clinical setting). Outcome was available for all cases in the validation cohort and for 521 in the clinical cohort. Cell-free DNA from plasma samples was sequenced using the Ion Proton sequencer, and sequencing data were analyzed using the open-access software, WISECONDOR. Performance metrics for detection of trisomies 21, 18 and 13 were calculated based on either fetal karyotype result or clinical data collected at birth. We also evaluated the failure rate and compared three methods of fetal fraction quantification (RASSF1A assay, and DEFRAG and SANEFALCON software). RESULTS: Results from both cohorts were consistent and their gestational age was not significantly different so their data were combined to increase the sample size for analysis. Sensitivities and specificities, respectively, were as follows: for trisomy 21, 98.3% (95% CI, 93.5-99.7%) and 99.9% (95% CI, 99.4-100%); for trisomy 18, 96.7% (95% CI, 80.9-99.8%) and 100% (95% CI, 99.6-100%); and for trisomy 13, 94.1% (95% CI, 69.2-99.7%) and 100% (95% CI, 99.6-100%). Our failure rate was 1.2% initially and as low as 0.6% after retesting some of the failed samples. Fetal fraction estimation by the RASSF1A assay was consistent with DEFRAG results, and both were adequate for routine diagnosis. CONCLUSIONS: We describe one of the largest studies evaluating Ion Proton-based NIPS and the first clinical study reporting pregnancy outcome in a large series of patients. This platform is highly efficient in detecting the three most common trisomies. Our protocol is robust and can be implemented easily in any medical genetics laboratory. Copyright © 2018 ISUOG. Published by John Wiley & Sons Ltd.

Muscle involvement in limb-girdle muscular dystrophy with GMPPB deficiency (LGMD2T).

OBJECTIVE: In this study, muscle involvement assessed by MRI and levels of GMPPB and glycosylation of α-dystroglycan expression in muscle were examined in patients with limb-girdle muscular dystrophy (LGMD) type 2T. METHODS: Six new patients with genetically verified mutations in GMPPB were studied. T1-weighted magnetic resonance images were obtained in 4 participants. Muscle strength and potential involvement of extramuscular organs were examined. Glycosylation of α-dystroglycan in muscle was studied, and GMPPB and α-dystroglycan expression was analyzed by Western blotting. Prevalence of LGMD2T was calculated from the total LGMD population in Denmark. GMPPB was sequenced in all unclassified cases. RESULTS: Two patients carried 3 new mutations in GMPPB. The other 4 patients carried previously described pathogenic mutations in GMPPB. MRI showed that the paraspinal muscles were the most affected, followed by involvement of hamstrings. Our results showed a loss of glycosylation of α-dystroglycan as well as secondary loss of merosin expression on Western blotting. The prevalence of LGMD2T in the Danish cohort of patients with LGMD is 1.5%. CONCLUSIONS: The new findings of this study are (1) the consistent finding of a preferential affection of paraspinal and hamstring muscles in LGMD2T, (2) 3 new mutations in GMPPB, (3) variable loss of glycosylation tested with IIH6 and VIA4 antibodies, and (4) a prevalence of LGMD2T of 1.5% in a well-characterized Danish LGMD cohort.

Cell cloning-based transcriptome analysis in Rett patients: relevance to the pathogenesis of Rett syndrome of new human MeCP2 target genes.

More than 90% of Rett syndrome (RTT) patients have heterozygous mutations in the X-linked methyl-CpG binding protein 2 (MECP2) gene that encodes the methyl-CpG-binding protein 2, a transcriptional modulator. Because MECP2 is subjected to X chromosome inactivation (XCI), girls with RTT either express the wild-type or mutant allele in each individual cell. To test the consequences of MECP2 mutations resulting from a genome-wide transcriptional dysregulation and to identify its target genes in a system that circumvents the functional mosaicism resulting from XCI, we carried out gene expression profiling of clonal populations derived from fibroblast primary cultures expressing exclusively either the wild-type or the mutant MECP2 allele. Clonal cultures were obtained from skin biopsy of three RTT patients carrying either a non-sense or a frameshift MECP2 mutation. For each patient, gene expression profiles of wild-type and mutant clones were compared by oligonucleotide expression microarray analysis. Firstly, clustering analysis classified the RTT patients according to their genetic background and MECP2 mutation. Secondly, expression profiling by microarray analysis and quantitative RT-PCR indicated four up-regulated genes and five down-regulated genes significantly dysregulated in all our statistical analysis, including excellent potential candidate genes for the understanding of the pathophysiology of this neurodevelopmental disease. Thirdly, chromatin immunoprecipitation analysis confirmed MeCP2 binding to respective CpG islands in three out of four up-regulated candidate genes and sequencing of bisulphite-converted DNA indicated that MeCP2 preferentially binds to methylated-DNA sequences. Most importantly, the finding that at least two of these genes (BMCC1 and RNF182) were shown to be involved in cell survival and/or apoptosis may suggest that impaired MeCP2 function could alter the survival of neurons thus compromising brain function without inducing cell death.

Novel FOXG1 mutations associated with the congenital variant of Rett syndrome.

BACKGROUND: Rett syndrome is a severe neurodevelopmental disorder representing one of the most common genetic causes of mental retardation in girls. The classic form is caused by MECP2 mutations. In two patients affected by the congenital variant of Rett we have recently identified mutations in the FOXG1 gene encoding a brain specific transcriptional repressor, essential for early development of the telencephalon. METHODS: 60 MECP2/CDKL5 mutation negative European Rett patients (classic and variants), 43 patients with encephalopathy with early onset seizures, and four atypical Rett patients were analysed for mutations in FOXG1. RESULTS AND CONCLUSIONS: Mutations have been identified in four patients, independently classified as congenital Rett variants from France, Spain and Latvia. Clinical data have been compared with the two previously reported patients with mutations in FOXG1. In all cases hypotonia, irresponsiveness and irritability were present in the neonatal period. At birth, head circumference was normal while a deceleration of growth was recognised soon afterwards, leading to severe microcephaly. Motor development was severely impaired and voluntary hand use was absent. In contrast with classic Rett, patients showed poor eye contact. Typical stereotypic hand movements with hand washing and hand mouthing activities were present continuously. Some patients showed abnormal movements of the tongue and jerky movements of the limbs. Brain magnetic resonance imaging showed corpus callosum hypoplasia in most cases, while epilepsy was a variable sign. Scoliosis was present and severe in the older patients. Neurovegetative symptoms typical of Rett were frequently present.

The p.Val66Met polymorphism in the BDNF gene protects against early seizures in Rett syndrome.

OBJECTIVE: X chromosome inactivation and the MECP2 genotype do not provide the full explanations for the clinical differences between patients with Rett syndrome (RTT), suggesting the involvement of other factors. One MeCP2 target is the brain-derived neurotrophic factor (BDNF) gene. We investigated, according to the MECP2 genotype, the role of the BDNF functional polymorphism (Val66Met) on the severity of RTT. METHODS: This polymorphism in BDNF was analyzed by PCR and dHPLC in 81 patients with RTT. We studied the association between the MECP2 and BDNF genotypes and the clinical features in each patient. RESULTS: We found that some RTT features can be correlated with MECP2 genotypes. Missense mutations are associated with a more severe epileptic phenotype (early onset and drug resistance) than other mutations. Non-sense and late truncating mutations lead to a less severe phenotype regarding walking. The distribution of the Val66Met polymorphism was not significantly different between the different groups in regard to the severity of all tested symptoms. However, girls with RTT bearing the Val66Val genotype tend to present earlier seizures than girls with RTT bearing the Met66 allele. No girls with RTT with the Met66 allele presented early seizures. CONCLUSIONS: Early onset of seizures is linked to the combined MECP2 and BDNF genotypes. The BDNF Met66 allele may protect against seizures, whereas missense mutations in the MBD of MECP2 are more frequently associated with early seizures.

Impairment of CDKL5 nuclear localisation as a cause for severe infantile encephalopathy.

Mutations in the human X-linked cyclin-dependent kinase-like 5 (CDKL5) gene have been shown to cause infantile spasms as well as Rett syndrome-like phenotype. To date, fewer than 20 different mutations have been reported. So far, no clear genotype-phenotype correlation has been established. We screened the entire coding region of CDKL5 in 151 affected girls with a clinically heterogeneous phenotype ranging from encephalopathy with epilepsy to atypical Rett syndrome by denaturing high liquid performance chromatography and direct sequencing, and we identified three novel missense mutations located in catalytic domain (p.Ala40Val, p.Arg65Gln, p.Leu220Pro). Segregation analysis showed that p.Arg65Gln was inherited from the healthy father, which rules out the involvement of CDKL5 in the aetiology of the phenotype in this patient. However, the de novo occurrence was shown for p.Ala40Val and p.Leu220Pro. The p.Ala40Val mutation was observed in two unrelated patients and represented the first recurrent mutation in the CDKL5 gene. For the two de novo mutations, we analysed the cellular localisation of the wild-type and CDKL5 mutants by transfection experiments. We showed that the two CDKL5 mutations cause mislocalisation of the mutant CDKL5 proteins in the cytoplasm. Interestingly these missense mutations that result in a mislocalisation of the CDKL5 protein are associated with severe developmental delay which was apparent within the first months of life characterised by early and generalised hypotonia, and autistic features, and as well as early infantile spasms.

Maternal origin of a novel C-terminal truncation mutation in CDKL5 causing a severe atypical form of Rett syndrome.

The CDKL5 gene has been implicated in infantile spasms and more recently in a Rett syndrome-like phenotype. We report a case of a young girl presenting generalized convulsions at 10 days of life. Subsequent mutation analysis by denaturing high-performance liquid chromatography of MECP2 and CDKL5 genes revealed heterozygosity for a c.47_48insAGG insertion in exon 1 of MECP2 and heterozygosity for a new nonsense mutation p.Q834X and a new missense variant p.V999M in the CDKL5 gene. Co-segregation analysis showed that the nonsense mutation was a de novo mutation and that the insertion and the missense variant were also found in the asymptomatic mother. In the absence of skewed X inactivation in the mother, it is likely that these last two variants are not pathogenic. Reverse transcription-polymerase chain reaction from lymphoblastoid cells of the patient showed only the transcript without the nonsense and missense variations suggesting decreased stability of mature mRNA by nonsense-mediated decay. These data also suggest an occurrence of the de novo mutation in maternal germ line cells. Moreover, this report reinforces the observation that the CDKL5 phenotype overlaps with Rett syndrome and that CDKL5 gene analysis is recommended in females with a seizure disorder commencing in the first weeks of life.

International incidence of childhood brain and spinal tumours.

BACKGROUND: Intracranial and spinal cord tumours are the second most frequent type of childhood cancer after leukaemia, accounting for around 20% of cases in many regions of the world, yet there have been few studies of their incidence by histological type and subsite. METHODS: Age-specific and age-adjusted incidence rates were calculated from data in the study, 'International Incidence of Childhood Cancer', co-ordinated by the International Agency for Research on Cancer. RESULTS: The highest age-adjusted incidence, 31.4 per million, was observed in the Nordic countries, and rates between 24 and 27 per million were found in most other predominantly white Caucasian populations. In the US, black children had a significantly lower incidence (21.7) than whites (26.4). Lower rates were seen in South America, Africa and Asia, the lowest being those for Chinese populations, and for blacks in Africa, both below 15 per million. Among white populations, astrocytomas were the commonest histological type, often with an incidence of at least 10 per million, followed by medulloblastomas, 5-6 per million, and ependymomas, 2-4 per million. In other regions with lower incidence rates, these three types accounted for similar proportions of the total. Black children in the US had a higher incidence of craniopharyngiomas than whites and there was an unusually high incidence of pineal tumours in Japan, 0.9 per million compared with 0.3-0.4 in many other countries. CONCLUSIONS: The low recorded total incidence in developing countries may be partly due to underascertainment. Differences in total incidence or in relative frequencies of particular histological types between Western countries and Japan and between ethnic groups in the US suggest a substantial contribution of genetic predisposition in their aetiology.

International variations in the incidence of childhood bone tumours.

Bone cancers comprise about 5% of childhood neoplasms. Osteosarcoma, the most common sub-type, shows a somewhat irregular geographic pattern of incidence, with low rates in some Asian (Indian, Japanese, Chinese) and Latin American populations. Incidence is similar in the sexes and rises steeply with age, accompanied by an increasing proportion of tumours localized in the long bones of the legs. Rates in the USA are higher in blacks than in whites, as a result of a higher incidence at ages 10 to 14 and of tumours of the leg bones. The descriptive epidemiology is consistent with early observations linking risk to the amount of bone growth. Ewing's sarcoma is rare in black populations (USA and Africa) and in eastern Asia. Compared with osteosarcoma, a lower percentage of tumours is localized to the long bones, and incidence rises less steeply with age and is accompanied by an increasing proportion of pelvic tumours. Chondrosarcoma is a rare cancer in children (less than 5% of bone cancers), with an age distribution similar to that of osteosarcoma and a sub-site distribution resembling that of Ewing's sarcoma. Little is known of the aetiology of these tumours; there is clearly a strong genetic predisposition in Ewing's sarcoma but, although the proportion of osteosarcoma cases of genetic origin seems to be small, environmental determinants so far suspected can account for only a small fraction of the total cases.

Trends in biliary tract cancer.

Incidence data from a large number of cancer registries throughout the world are presented for cancers at various sub-sites of the biliary tract, to assess whether the epidemiology of gall bladder cancer can be distinguished from cancer of the extra-hepatic bile ducts and cancer of the ampulla of Vater. Cancers of the biliary tract appear to be strongly sex-related. A marked genetic susceptibility emerges from this review, not only for gall bladder cancer, as previously reported for American Indians, but also perhaps for cancer of the extrahepatic bile ducts, for which Japanese of both sexes have high rates. Mortality data for all biliary tract (mainly gall bladder) cancer are examined for the period 1958-85. A wide range of trends is observed, notably a consistent decline in mortality among Anglo-Saxon populations, for both males and females. Dietary factors, possibly mediated through hormonal and genetic factors, are suggested as a major causal influence on biliary tract cancers.

[Epidemiology of breast cancer in men]. / L'épidémiologie du cancer du sein chez l'homme.

Incidence data for male breast cancer from 34 selected cancer registries in different parts of the world are presented. The geographic variation in incidence is similar to that observed for female breast cancer, resulting in a strong correlation between their respective rates, although certain populations have higher rates for male breast cancer than expected from the female incidence, notably Israeli Jews and blacks in the United States. It seems that both environmental factors (acting by the intermediary of endogenous oestrogens excess) and genetic predisposition play a role in determining the epidemiological profile of male breast cancer, as they do for cancer of the female breast.

Temporal change in diagnostic criteria as a cause of the increase of malignant melanoma over time is unlikely.

To assess whether the increase in malignant melanoma incidence could be due, at least in part, to changes in histological criteria of malignancy, pathologists in Australia, France, Italy, New Zealand, Norway, Sweden, the United Kingdom, the United States and the USSR reviewed diagnoses of 50 consecutive pigmented naevi (40 junctional and compound; 10 intradermal) and 20 consecutive malignant melanomas made in each participating centre around 1930, around 1955 and around 1980. Collaborating pathologists re-read the material, 2,665 cases in all, either from the original slide (82%) or from a recut block (17%), gave their diagnosis and indicated whether the lesion was benign (B), dubious benign (DB), dubious malignant (DM) or malignant (M). As the distribution of review diagnoses was much the same whether the original slide or one made from a recut block was read, the material was pooled. Overall, 2.8% of cases originally reported as B/DB were reviewed as DM/M, while 4.4% of the DM/M diagnoses were held to be B/DB. The shifts between categories were greatest around 1955 and least around 1980, suggesting increasing uniformity of interpretation. All available blocks were recut and sections sent to IARC for review: 1.7% (22) of 1293 B/DB diagnoses were considered to be DM/M and 3.3% (18) of 551 DM/M diagnoses were considered to have been B/DB. The consistently low frequency of shift in diagnostic category, whether the material was reviewed in the collaborating laboratories or by one pathologist at IARC, in a study designed to give maximum attention to those lesions--the junctional and compound naevi--in which a change in opinion as to malignancy would be most likely to arise, suggests that pathologists, irrespective of geographical location, are using common criteria. These findings argue against changes in histological interpretation as being responsible for more than a small portion of the continuous increase of some 3% to 8% per annum observed in malignant melanoma incidence. Other explanations, such as an increase in the frequency or potential for malignant transformation of precursor lesions, must be sought. The anatomical distribution of the malignant melanomas examined followed the usual site pattern by sex, and their thickness was observed to decrease over the period of the study in most centres.

The epidemiology of prostatic cancer. Geographical distribution and time-trends.

Prostate cancer is one of the most frequent tumours in males. Globally about 235,000 new cases were estimated to occur in 1980. The cancer is particularly frequent in North America, where rates in blacks are often double those in whites, and in several European countries, being rare in much of Asia. After migration to the US, Chinese and Japanese show substantial increases. Incidence may be distorted by inclusion of varying numbers of so-called 'latent' cancers; for some comparisons mortality data are preferable. 'Small' latent cancers seem to be uniformly distributed irrespective of the incidence of the clinically manifest form. The incidence of prostate cancer seems to be increasing in most populations, particularly in Asia and Eastern Europe. In general, mortality follows suit. Birth cohort analysis shows that for US non-whites, cohorts born before 1896-1900 showed an increase in mortality for all age groups, but the death rates fell for cohorts born subsequently, a phenomenon also observed in Australia and England and Wales.

[Geographic distribution of cancer of the larynx and hypopharynx by anatomic subsite]. / Les variations géographiques des cancers du larynx et de l'hypopharynx par sous-localisation anatomique.

Incidence data from many cancer registries throughout the world are presented for the major sub-sites of laryngeal and hypopharyngeal cancers. Correlations between glottic (161.0) supra-glottic (161.1) and pyriform sinus (148.1) cancers, and cancers at sites known to be associated with tobacco and alcohol on the one hand, and to annual tobacco and alcohol consumption on the other, are examined. The major role of alcohol in males, suggested by previous studies, is confirmed, but the effect of tobacco does not emerge at population level.

[Incidence of cancer in children throughout the world]. / L'incidence des cancers de l'enfant dans le monde.

The International Agency for Research on Cancer has coordinated a worldwide study of the incidence of cancer in childhood. Contributors from over 50 countries have provided data. This paper presents a summary of some of the major results. The incidence rates and relative frequencies of childhood cancers are described according to 12 diagnostic groups, defined mainly in terms of tumour morphology. Variations in the risk of those tumours between different countries and different ethnic groups provide important information on the relative importance of environmental and genetic factors in their aetiology.

Descriptive epidemiology of malignant neoplasms of nose, nasal cavities, middle ear and accessory sinuses.

International incidence and mortality data for ICD rubric 160 (nose and nasal cavities, middle ear and accessory sinuses) are reviewed, the relative frequency data for cancer for each of the constituent anatomical locations presented and the histological types of neoplasms encountered tabulated to determine if geographical differences exist which might be worth further investigation. Relatively high rates for this generally rare disease were found in Asian and African populations, the highest age-adjusted rates, between 2.6 and 2.5 per 100,000 per annum, occurring in Japanese males. Independent of the higher rates, the extremely low proportion of cancers of the nose and nasal cavities together with the very high proportion of cancer of the maxillary sinus in Japan are in contrast with a much higher relative frequency of nose and nasal cavity cancer in other countries. These findings seem to justify further studies of these tumours in this country, particularly as none of the known aetiological factors reviewed in this paper explain the high rates for this cancer in Japan.