Search

Introduction: Coffin-Siris syndrome (CSS) (MIM #135900) is an extremely rare genetic multisystemic disorder characterized by aplasia or hypoplasia of the upper phalanx of the fifth finger, moderate to severe cognitive and/or developmental delay, and characteristic facial features (thick lashes, hypertrichosis of the trunk, sparse hair). Congenital anomalies of the brain, kidney, and heart have been described but are less consistent across patients. Case presentation: We report a case of a 12-year-5-month-old girl with the clinical features of CSS, severe scoliosis, and epilepsy. Growth hormone deficiency was diagnosed at the age of 9 years. Recombinant human growth hormone (rhGH) treatment was started that resulted in a significant improvement of the growth velocity up to 5.4 cm/year (>90-97th centile). Next-generation sequencing identified a mutation in the ARID1B gene. Discusion: Despite its phenotypic heterogeneity, key features of CSS have become clearer and along with molecular diagnosis, a further global approach to improve the care of these individuals is enabled. Appropriate therapies for this population are needed to optimize growth and intellectual potentials.

Highlights A novel heterozygous mutation in the SLC5A2 gene in a 2-year-old girl with severe asymptomatic glycosuria, mild failure to thrive, and subclinical hypoglycemia: Continuous glucose monitoring identified 14% hypoglycemic excursions (< 70 mg/dl), reduced at 1% with 1 g/Kg uncooked cornstarch at bed-time milk and eliminated (0%) adjusting the dose at 1.5 g/Kg, as shown by Flash technology.

Snyder-Robinson syndrome (SRS) is an extremely rare X-linked intellectual disability syndrome (MRXSSR; MIM #309583). The main clinical features of SRS include psychomotor delay, hypotonia, and asthenic-type body habitus – reduced body weight and bone abnormalities (osteoporosis, fractures, kyphoscoliosis). We report a case of SRS with a hemizygous missense variant in the SMS gene,c.334C>G (p.Pro112Ala), in a 4-year-old boy, who initially developed hypotonia, delayed motor skills, and subsequently epilepsy. This variant in SMS was found to be de novo. To the best of our knowledge, this novel SMS gene variant has never been previously reported in disease-related variation databases, such as ClinVar or HGMD.

Mutations in the skeletal muscle ryanodine receptor (RYR1) gene have been linked to malignant hyperthermia susceptibility, central core disease, and minicore myopathy with external ophthalmoplegia. RYR1 is an intracellular calcium release channel and plays a crucial role in the sarcoplasmic reticulum and transverse tubule connection. Here, we report 2 fetuses from the same parents with compound heterozygous mutations in the RYR1 gene (c.10347+1G>A and c.10456-2Α>G) who presented with fetal akinesia and polyhydramnios at 27 and 19 weeks of gestation with intrauterine growth restriction in the third pregnancy. The prospective parents of the fetuses were heterozygous carriers for c.10456-2Α>G (mother) and c.10347+1G>A (father). Both mutations affect splice sites resulting in dysfunctional protein forms probably missing crucial domains of the C-terminus. Our findings reveal a new RYR1 splice site mutation (c.10456-2Α>G) that may be associated with the clinical features of myopathies, expanding the RYR1 spectrum related to these pathologies.

Τα μικρά υπεράριθμα χρωμοσώματα-δείκτες (sSMCs) ορίζονται ως δομικές χρωμοσωμικές ανωμαλίες, μεγέθους ίσου ή μικρότερου από το χρωμόσωμα 20 που δεν μπορούν να χαρακτηρισθούν και να ταυτοποιηθούν με τις κλασικές κυτταρογενετικές τεχνικές. Ένα sSMC μπορεί να εμφανίζεται σε καρυότυπο με (1) 46 φυσιολογικά χρωμοσώματα, (2) αριθμητικές ανωμαλίες (π.χ. Turner syndrome ή Down syndrome), ή (3) δομικές ισοζυγισμένες ανωμαλίες. Τα sSMCs εμφανίζονται με συχνότητα 0.075% σε μη επιλεγμένα περιστατικά προγεννητικού ελέγχου ενώ μόνο 0.044% σε μεταγεννητικά περιστατικά. Η συχνότητα των sSMC στα περιστατικά προγεννητικού ελέγχου με υπερηχογραφικές ανωμαλίες είναι τουλάχιστον πέντε φορές μεγαλύτερη από ότι στα νεογνά και τουλάχιστον τρεις φορές υψηλότερη από ότι στα μη επιλεγμένα προγεννητικά περιστατικά. Επίσης 0.288% των ασθενών με αναπτυξιακή/νοητική υστέρηση έχουν ένα sSMC. Περίπου το 70% των de novo sSMC δεν έχει φαινοτυπικές επιπτώσεις. Ο κίνδυνος για φαινοτυπικές ανωμαλίες σε περιπτώσεις προγεννητικής εντόπισης ανέρχεται περίπου στο 13%. Αυτό εξαρτάται τόσο από την προέλευση του χρωμοσώματος-δείκτη, όσο και από το εάν εμφανίζεται για πρώτη φορά στο έμβρυο (de novo), ή είναι οικογενής (familial). Ο κίνδυνος μπορεί να κυμαίνεται από 7% όταν το de novo sSMCs προέρχεται από τα χρωμοσώματα 13, 14, 15, 21 και 22, έως το 28% για τα μη ακροκεντρικά χρωμοσώματα. Επίσης, περισσότερα από 98% των κληρονομούμενων sSMC είναι χωρίς φαινοτυπικές επιπτώσεις. Στον προγεννητικό έλεγχο το 16% των sSMC έχει κλινικές επιπτώσεις. Πιο συγκεκριμένα ο κίνδυνος για φαινοτυπικές ανωμαλίες ανέρχεται στο 10.9% για τα sSMC που προέρχονται από ακροκεντικά χρωμοσώματα και φθάνει στο 14% για τα μη ακροκεντρικά sSMC.Δεν γνωρίζουμε πάρα πολλά σχετικά με τον ακριβή τρόπο σχηματισμού των sSMC και είναι ιδιαίτερα ασαφές, πού, γιατί και πότε δημιουργείται ένα sSMC, κατά την διάρκεια της γαμετογένεσης ή της εμβρυογένεσης. Πάντως, υπάρχουν διάφορα μοντέλα του πώς δημιουργούνται οι διάφορες μορφές sSMC. Αυτές οι θεωρίες βασίζονται στα ευρήματα από το UPD και στην παρατήρηση ότι τα sSMCs μπορεί να δημιουργούνται από ατελή διόρθωση της τρισωμίας. Συνολικά, ένα sSMC σχηματίζεται από τον συνδυασμό δύο ή περισσοτέρων συμβάντων κατά της διάρκεια της γαμετογένεσης ή της εμβρυογένεσης.Κλασικά, η παρουσία ενός sSMC σε ένα ασθενή τεκμηριώνεται με την ζώνωση και ανάλυσή των χρωμοσωμάτων, είτε στο περιφερικό αίμα, είτε στο αμνιακό υγρό ή στις χοριακές λάχνες. Εάν με την κυτταρογενετική ανάλυση παρατηρηθεί ένα sSMC, τότε αυτό πρέπει να χαρακτηρισθεί περαιτέρω με μοριακές κυτταρογενετικές τεχνικές. Σήμερα με την ανάπτυξη της μοριακής κυτταρογενετικής και την χρήση των array-CGH μπορούν να χαρακτηριστούν σχεδόν όλες οι χρωμοσωμικές ανισοζυγίες.Ο σκοπός της παρούσας μελέτης ήταν να διερευνηθούν πλήρως τα sSMCs που εντοπίζονται σε δείγματα προγεννητικού ελέγχου, προκειμένου να δοθεί σωστή πρόγνωση και γενετική συμβουλευτική. Απώτερος στόχος της μελέτης ήταν να γίνει συσχέτιση του γονότυπου με το φαινότυπο, και ειδικότερα με τα υπερηχογραφικά ευρήματα αλλά και την κλινική εικόνα του νεογνού σε περιπτώσεις συνέχισης της κύησης. Συγκεκριμένα, η μελέτη εστιάστηκε στο χαρακτηρισμό και ταυτοποίηση των χρωμοσωμάτων δεικτών σε δείγματα προγεννητικού ελέγχου και συγχρόνως στη μελέτη της παρουσίας ή όχι ευχρωματικής περιοχής, εφαρμόζοντας τεχνικές κλασικής κυτταρογενετικής και τεχνικές μοριακής κυτταρογενετικής (φθορίζων in situ υβριδισμός, FISH και array-CGH).Παράλληλα μελετήθηκε η παρουσία ή όχι μονογονεϊκής δισωμίας (UPD), εστιάζοντας στα χρωμοσώματα δείκτες των οποίων η προέλευσή ήταν από χρωμοσώματα που εμπλέκονται σε μονογονεϊκή δισωμία. Για το σκοπό αυτό έγινε μοριακή ανάλυση για την ύπαρξη ή όχι μονογονεϊκής δισωμίας στα περιστατικά με υπεράριθμο μικρό χρωμόσωμα-δείκτη που έχουν αυξημένο κίνδυνο για UPD. Χαρακτηρίσθηκαν επιτυχώς 42 χρωμοσώματα δείκτες που εντοπίσθηκαν σε περίπου 50.000 προγεννητικά δείγματα αμνιακού υγρού και χοριακών λαχνών. Τα αποτελέσματα της παρούσας διδακτορικής διατριβής, ανέδειξαν τη συμβολή των μοριακών κυτταρογενετικών τεχνικών (FISH και array-CGH) στον ακριβή χαρακτηρισμό των μικρών χρωμοσωμάτων – δεικτών μετά τον εντοπισμό τους στον προγεννητικό έλεγχο. Χρησιμοποιώντας τεχνικές FISH και array-CGH στην παρούσα μελέτη κατορθώσαμε να χαρακτηρίσουμε επιτυχώς και τα 42 sSMCs που ανιχνεύθηκαν με την κλασσική κυτταρογενετική. Εκτός από την χρωμοσωμική προέλευση του sSMC προσδιορίσθηκε η παρουσία ή όχι ευχρωματίνης, το μέγεθος αυτής και ο αριθμός των γονιδίων που περιέχει. Συνολικά 19/42 (45%) περιπτώσεις από την συγκεκριμένη μελέτη συνδέονται με σημαντικά κλινικά ευρήματα. Αποτέλεσμα αυτών είναι να δοθούν σωστές γενετικές συμβουλές στα ζευγάρια.Στη παρούσα μελέτη εάν χρησιμοποιείτο μόνο η τεχνική array-CGH δεν θα είχαν ανιχνευθεί 16 περιπτώσεις sSMCs που αποτελούντο αποκλειστικά από ετεροχρωματικό υλικό. Στις 12/16 περιπτώσεις τo sSMC προέρχονταν από χρωμοσώματα όπως το 14 ή το 15 που ήταν απαραίτητη η ανάλυση UPD. Αντίθετα η μη χρησιμοποίηση των array-CGH δεν θα αποκάλυπτε την πολυπλοκότητα κάποιων sSMCs ούτε τον λεπτομερή χαρακτηρισμό αυτών των sSMCs, με αποτέλεσμα να μην υπάρχει σαφής εικόνα για την πρόγνωση και την γενετική συμβουλευτική. Η εκτεταμένη εφαρμογή του array-CGH αποκαλύπτει περισσότερες εκπλήξεις και πιθανόν να διαφοροποιηθεί η άποψη σχετικά με τη σύνθεση των υπεράριθμων χρωμοσωμάτων δείκτων. Συμπερασματικά η μοριακή κυτταρογενετική (FISH, array-CGH) σε συνδυασμό με άλλες μοριακές τεχνικές (UPD) μπορεί να παράσχει πολύτιμες πληροφορίες σχετικά με την χρωμοσωμική προέλευση και τη σύνθεση των χρωμοσωμάτων δεικτών στην προγεννητική διάγνωση. Με τη νέα τεχνολογία array-CGH είναι δυνατό να χαρακτηριστεί πλήρως το γενετικό περιεχόμενο του κάθε δείκτη και, σε ειδικές περιπτώσεις, να περιγραφεί και να προβλεφθεί ο πιθανός κλινικός φαινότυπος.

MCPH1, otherwise known as the microcephalin gene (*607117) and protein, is a basic regulator of chromosome condensation (BCRT-BRCA1 C-terminus). The Microcephalin protein is made up of three BCRT domains and conserved tandem repeats of interacting phospho-peptide. There is a strong connection between mutations of the MCPH1 and reduced brain growth. Specifically, individuals with such mutations have underdeveloped brains which means smaller size, varying levels of mental retardation, delayed speech and poor language skills, individuals with mild microcephaly and normal intelligence notwithstanding. In this case, a fetus with novel homozygous mutation of the MCPH1 gene ((c.348del)), whose parents were recessive heterozygous for (c.348del), displayed severe microcephaly at 22 weeks of gestation. Due to the effect on splice sites in introns, this mutation causes forming of dysfunctional proteins which lack crucial domains of the C-terminus. Our findings portray an association between the new MCPH1 mutation ((c.348del)) and the clinical features of autosomal recessive primary microcephaly (MCPH) contributing to a broader spectrum related to these pathologies.

Baraitser - Winter Cerebrofrontofacial Syndrome (BWCFF) is a rare disorder characterized by facial dysmorphism and mental retardation of varying grades. The clinical phenotype of BWCFF indicates variable phenotypic expression involving various congenital malformations such as cardiac, renal and musculoskeletal abnormalities. Nevertheless, the prenatal presentation of BWCFF is rarely described, making prenatal diagnosis challenging. This report describes a prenatal diagnosis of BWCFF syndrome to date; a case of a fetus with intrauterine growth restriction, increased nuchal fold, bilateral hydronerphosis, rocker bottom foot and clubfoot detected on Anomaly Scan is outlined. Molecular karyotype failed to detect any abnormality. Assessment with Next Generation Sequencing was then performed, revealing a heterozygous de novo mutation in ACTB gene setting the diagnosis of BWCFF.

Background The interstitial 6p22.3 deletions concern rare chromosomal events affecting numerous aspects of both physical and mental development. The syndrome is characterized by partial deletion of chromosome 6, which may arise in a number of ways. Case presentation We report a 2.8-year old boy presenting with developmental delay and mild dysmorphisms. High-resolution oligonucleotide microarray analysis revealed with high precision a 2.5 Mb interstitial 6p deletion in the 6p22.3 region which encompasses 13 genes. Conclusions Identification and in-depth analysis of cases presenting with mild features of the syndrome will sharpen our understanding of the genetic spectrum of the 6p22.3 deletion.

Background: Idiopathic early-onset central diabetes insipidus (CDI) may be due to mutations of arginine vasopressin-neurophysin II (AVP-NPII (AVP)) or wolframin (WFS1/2) genes (1). Clinical Case: A 4-month old girl presented to our pediatric endocrinology clinic due to severe polydipsia-polyphagia and polyuria. Plasma and urine glucose and HbA1c were normal and 24h monitoring of urinary output was elevated (4.2ml/kg/h). We proceeded to a modified 5-h water deprivation test followed by 0.1 mcg DDAVP IM. Results were compatible with partial central DI: at 5-hrs weight loss 5%, urine osmolality 155 from 111 at 0΄and 355 mOsm/kg 2hrs after DDAVP administration. Pituitary MRI was normal with presence of posterior pituitary bright spot and normal pituitary stalk. We initiated therapy with oral desmopressin acetate titrated at the dose of 70mcg x 3/day under close clinical and biochemical surveillance. Hyponatremia, with high natriuresis >100 mmol/L and elevated BNP occurred the 3rd day. Fludrocortisone 100 mcg x 2/day controlled natriuresis and supplemental oral NaCl 15% 15ml/day was needed to restore normal electrolytes (2). Marked catch-up growth was observed already at 1 month for height, weight and head circumference. Methods: Whole exome sequencing was performed targeted to a gene panel related to DI, containing AVP gene, WFS1/2 genes and AVPR2/AQP2 genes. Result: Two heterozygous variants were revealed: WFS1:NM_001145853:exon8:c. G997A:p.V333I,WFS1:NM_006005:exon8:c.G997A:p.V333I and WFS1:NM_00114585 3:exon8:c.G1832A:p.R611H,WFS1:NM_006005:exon8:c.G1832A:p.R611H reported as possibly damaging in 1/6 and 4/6 prediction programs respectively. These variants will be checked in both parents to confirm the presumed compound heterozygosity pattern in the child. Conclusion: We present a 4-month old girl with two heterozygous variants of WFS1 gene which may cause early-onset central diabetes insipidus and possibly a WFS1 related disorder (1). Reference: (1) Perrotta S et al. Early-onset central diabetes insipidus is associated with de novo arginine vasopressin-neurophysin II or Wolfram syndrome 1 gene mutations. Eur J Endocrinol. 2015 Apr;172(4):461-72 (2) Papadimitriou DT, Spiteri A, Attilakos A, Papadimitriou A. Cerebral Salt Wasting Complicated by Central Diabetes Insipidus and Growth Hormone Deficiency. Indian J Pediatr. 2018 Jul;85(7):580-581

Background: Micropenis is caused either by a defect in androgen synthesis, conversion to Dihydrotestosterone, or action due to mutant androgen receptor. Premature adrenarche is caused by excess of adrenal androgens. Clinical case: A 6,5-year-old boy presented to our pediatric endocrinology clinic due to increased body weight and hyperthyreotropinemia. Physical examination revealed premature adrenarche with testicular volume 1,5 ml, micropenis (4cm, Laboratory investigations for premature adrenarche with synacthen test revealed mild elevation of compound-S 15,4 ng/dl at 60’, which could be theoretically attributed to partial 11-β-hydroxylase deficiency (CYP11B1). DHEA was also elevated 2,1 ng/ml with an increased DHEA/Δ4 ratio at 20 (normal < 10) which could be explained in the case of partial 3-β-Hydroxysteroid dehydrogenase deficiency. Method: Whole exome sequencing was preformed targeted to a gene panel related to premature adrenarche. Results: A heterozygous mutation c.[1174C>T]+[1174C>T]; p.[Pro329Ser]+[Pro329Ser] in exon 1 in Androgen Receptor (AR) gene (X-linked) was found to the patient and his mother. The mutation, according to Human Gene Mutation Database, can cause disorder of sex development (DSD), partial androgen insensitivity syndrome (PAIS), infertility and hypospadias. Additionally, sequencing of the coding region of the P450 oxyreductase (POR) gene revealed a heterozygous mutation c.[642-5C>G] in exon 7, which in homozygosity can cause steroidogenesis disorder due to oxyreductase deficiency. This heterozygous POR mutation was found to the patient and his father. Discussion: Our patient caries mutations in the AR and in POR genes. The AR mutation is obviously responsible for micropenis in our patient. CYP11B1 and 3β-Hydroxysteroid dehydrogenase genes were normal. POR deficiency is a disorder of steroidogenesis with phenotypic spectrum ranging from PCOS to ambiguous genitalia and glycocorticosteroid deficiency or even to classic Antley-Bixler syndrome (1). Conclusion: The genetic and hormonal results in our case imply a role for POR in the CYP11B1 gene expression, which is reported for the first time to our knowledge. 1. Concomitant Mutations in the P450 Oxidoreductase and Androgen Receptor Genes Presenting with 46,XY Disordered Sex Development and Androgenization at Adrenarche. J Clin Endocrinol Metab. 2010 Jul; 95(7): 3418-3427

Mutations in the skeletal muscle ryanodine receptor (RYR1) gene have been linked to malignant hyperthermia susceptibility, central core disease, and minicore myopathy with external ophthalmoplegia. RYR1 is an intracellular calcium release channel and plays a crucial role in the sarcoplasmic reticulum and transverse tubule connection. Here, we report 2 fetuses from the same parents with compound heterozygous mutations in the RYR1 gene (c.10347+1G>A and c.10456-2Α>G) who presented with fetal akinesia and polyhydramnios at 27 and 19 weeks of gestation with intrauterine growth restriction in the third pregnancy. The prospective parents of the fetuses were heterozygous carriers for c.10456-2Α>G (mother) and c.10347+1G>A (father). Both mutations affect splice sites resulting in dysfunctional protein forms probably missing crucial domains of the C-terminus. Our findings reveal a new RYR1 splice site mutation (c.10456-2Α>G) that may be associated with the clinical features of myopathies, expanding the RYR1 spectrum related to these pathologies.

Given the limited lifespan and with the recent progress in experimental treatments for WS, timely diagnosis and multidisciplinary treatment for DI/DM, hydronephrosis, and visual/psychiatric status—maintaining quality of life—are of crucial importance.

Holoprosencephaly (HPE) spectrum disorder is the most common congenital malformation of the human brain with absence of or incomplete midline cleavage. Its cause is heterogenic, making genetic counseling a challenge. In this case report, a pregnancy affected by alobar HPE is described. Using aCGH, an 8.9-Mb deletion at 7q36.1q36.3 together with a 4.9-Mb duplication at 12q24.32q24.33 is assumed to be the possible reason for this alobar HPE case. It is discussed that disruption of key elements of the developing brain, taking environmental factors into account, contributes to the HPE spectrum. The use of aCGH for invasive prenatal testing is starting to become the standard technique, providing accurate information about the cause of congenital diseases for couples receiving genetic counseling.

Whole exome sequencing (WES) has made the identification of causative SNVs/InDels associated with rare Mendelian conditions increasingly accessible. Incorporation of softwares allowing CNVs detection into the WES bioinformatics pipelines may increase the diagnostic yield. However, no standard protocols for this analysis are so far available and CNVs in non-coding regions are totally missed by WES, in spite of their possible role in the regulation of the flanking genes expression. So, in a number of cases the diagnostic workflow contemplates an initial investigation by genomic arrays followed, in the negative cases, by WES. The opposite workflow may also be applied, according to the familial segregation of the disease. We show preliminary results for a diagnostic application of a single next generation sequencing panel permitting the concurrent detection of LOH and variations in sequences and copy number. This approach allowed us to highlight compound heterozygosity for a CNV and a sequence variant in a number of cases, the duplication of a non-coding region responsible for sex reversal, and a whole-chromosome isodisomy causing reduction to homozygosity for a WFS1 variant. Moreover, the panel enabled us to detect deletions, duplications, and amplifications with sensitivity comparable to that of the most widely used array-CGH platforms.

Objective To calculate the proportion of array comparative genomic hybridization (aCGH) pathogenic results, that would not be detectable by non-invasive prenatal screening (NIPS). Methods This is a comparative study using data from 2779 fetuses, which underwent invasive prenatal diagnosis, and the samples were analyzed using aCGH. The simulated NIPS assay would test for trisomies 21, 18, 13, monosomy X, 47, XXX, 47, XYY, and 47, XXY. Indications for invasive testing were grouped into categories and the absolute, relative rates of pathogenic/likely pathogenic results of aCGH analysis that would not be detectable by NIPS were calculated. Results The expected rate of aCGH-detected abnormalities that would not be detectable by NIPS was 28.0% (95% CI 14.3–47.6) for nuchal translucency (NT) 95 to 99th centile; 14.3% (95% 5.0–34.6) for NT > 99th centile; 34.2% (95% CI 21.1–50.1) for high-risk first-trimester results (regardless of NT); 52.4% (95% CI 32.4–71.7) for second-trimester markers; and 50.0% (95% CI 26.8–73.2) for advanced maternal age. The overall rate of aCGH pathogenic/likely pathogenic results was 5.0% and 44.0% (95% CI 36.0–52.2) of them would not be detected by NIPS. Conclusions Approximately half of the abnormal aCGH results would not be detectable by standard NIPS assays, highlighting the necessity of pre-test counseling, and illustrating the limitations of NIPS. © 2017 John Wiley & Sons, Ltd.

In this report, a patient carrying a 650 kb deletion and a 759 kb duplication of chromosomal 21q22.3 region was described. Facial dysmorphic features, hypotonia, short stature, learning impairment, autism spectrum disorder, anxiety and depression were observed clinical characteristics. Mentioned copy number variants were the shortest in length reported so far. The current study hypothesized that the presence of a susceptibility locus for autism spectrum disorder associated with depression and anxiety may be located in a 200 kb region between the PCNT and PRMT2 genes. The current study aimed to provide insight into the human genome morbidity map of chromosome 21.

Treacher Collins syndrome (TCS) is a type of mandibulofacial dysostosis with incomplete penetrance and high intra- and interfamilial clinical heterogeneity, and it is associated with mutations of treacle ribosome biogenesis factor 1 (TCOF1), and RNA polymerase I and III subunit (POLR1)C and POLR1D genes. In the present case report, a patient with TCS with auricle dysplasia and hearing loss accompanied with intellectual disability is described. Sequence analysis was performed on blood samples from the patient and his father via oligonucleotide-based target capture, followed by next-generation sequencing. Alignment and variant calls were generated using the Burrows-Wheeler Aligner and Genome Analysis Toolkit, followed by bioinformatics analysis of the detected variants. A novel heterozygous mutation, c.911C>T (p.Ser304Leu), was detected in the TCOF1 gene, which was inherited from the father. The father of the patient only suffered from hearing loss. The present report is the first to identify an association between phenotypic variability and TCOF1 gene mutations and thus contributes to our understanding of the association between the genotype and phenotype in patients with TCS and offers clinically relevant information for diagnosis of the syndrome.

Background Non-invasive prenatal testing (NIPT) has been widely adopted for the detection of fetal aneuploidies and microdeletion syndromes, nevertheless, limited clinical utilization has been reported for the non-invasive prenatal screening of monogenic diseases. In this study, we present the development and validation of a single comprehensive NIPT for prenatal screening of chromosomal aneuploidies, microdeletions and 50 autosomal recessive disorders associated with severe or moderate clinical phenotype. Results We employed a targeted capture enrichment technology powered by custom TArget Capture Sequences (TACS) and multi-engine bioinformatics analysis pipeline to develop and validate a novel NIPT test. This test was validated using 2033 cell-fee DNA (cfDNA) samples from maternal plasma of pregnant women referred for NIPT and paternal genomic DNA. Additionally, 200 amniotic fluid and CVS samples were used for validation purposes. All NIPT samples were correctly classified exhibiting 100% sensitivity (CI 89.7–100%) and 100% specificity (CI 99.8–100%) for chromosomal aneuploidies and microdeletions. Furthermore, 613 targeted causative mutations, of which 87 were unique, corresponding to 21 monogenic diseases, were identified. For the validation of the assay for prenatal diagnosis purposes, all aneuploidies, microdeletions and point mutations were correctly detected in all 200 amniotic fluid and CVS samples. Conclusions We present a NIPT for aneuploidies, microdeletions, and monogenic disorders. To our knowledge this is the first time that such a comprehensive NIPT is available for clinical implementation.

We studied by a whole genomic approach and trios genotyping, 12 de novo, nonrecurrent small supernumerary marker chromosomes (sSMC), detected as mosaics during pre- or postnatal diagnosis and associated with increased maternal age. Four sSMCs contained pericentromeric portions only, whereas eight had additional non-contiguous portions of the same chromosome, assembled together in a disordered fashion by repair-based mechanisms in a chromothriptic event. Maternal hetero/isodisomy was detected with a paternal origin of the sSMC in some cases, whereas in others two maternal alleles in the sSMC region and biparental haplotypes of the homologs were detected. In other cases, the homologs were biparental while the sSMC had the same haplotype of the maternally inherited chromosome. These findings strongly suggest that most sSMCs are the result of a multiple-step mechanism, initiated by maternal meiotic nondisjunction followed by postzygotic anaphase lagging of the supernumerary chromosome and its subsequent chromothripsis.

To date, 6 cases of 17p13.1 microduplications have been described in the literature. Intellectual disability is the core feature, together with minor facial dysmorphisms and obesity. We describe the first case of a young patient with a maternally inherited microduplication in 17p13.1 presenting with growth hormone deficiency. The boy was addressed to the endocrine division for growth retardation (weight and height

Background Copy number variants (CNVs) are the genetic bases for microdeletion/ microduplication syndromes (MMSs). Couples with an affected child and desire to have further children are routinely tested for a potential parental origin of a specific CNV either by molecular karyotyping or by two color fluorescence in situ hybridization (FISH), yet. In the latter case a critical region probe (CRP) is combined with a control probe for identification of the chromosome in question. However, CNVs can arise also due to other reasons, like a recombination-event based on a submicroscopic, cryptic inversion in one of the parents. Results Seventy-four patients with different MMSs and overall 81 CNVs were studied here by a novel three color FISH approach. The way how three locus-specific probes are selected (one is the CRP and two are flanking it in a distance of 5-10 Mb) enables to detect or exclude two possible parental conditions as origins of the CNV seen in the index: (i) direct parental origin of the CNV (deletion or duplication) or (ii) a parental cryptic inversion. Thus, for overall 51/81 CNVs (63%) a parental origin could be determined. 36/51 (70.5%) inherited the CNV directly from one of the parents, but 15/51 (29.5%) were due to an exclusively by three color FISH detectable parental inversion. A 2:1 ratio of maternal versus paternal inheritance was found. Also almost two times more male than female were among the index patients. Conclusion The new, here suggested three color FISH approach is suited for more comprehensive parental studies of patients with MMS. The detection rate for parental origin was increased by 140% in this study. Still, for 30/81 cases (37%) no reason for the ‘de novo’ MMS in the affected index patient could be found by the here suggested FISH-probe set. Electronic supplementary material The online version of this article (10.1186/s13039-018-0369-1) contains supplementary material, which is available to authorized users.

Objective This study aims to evaluate the diagnostic yield of comparative genomic hybridization microarrays (aCGH) and compare it with conventional karyotype analysis of standard >5-Mb resolution. Method A total of 1763 prenatal samples were analyzed by aCGH (CytoChip Focus Constitutional microarrays, BlueGnome, Cambridge). The diagnostic yield of chromosomal abnormalities detected by aCGH was assessed, compared with conventional karyotype analysis. Results The result was pathogenic/unknown penetrance in 125 cases (7.1%), and a variant of unknown significance (VOUS) was detected in 13 cases (0.7%). Out of the 125 cases with abnormal findings, 110 were also detected by conventional karyotype analysis. The aCGH increment in diagnostic yield was 0.9% (15/1763) and 1.6% when VOUS were included. Stratifying the sample according to indications for prenatal invasive testing, the highest values of diagnostic yield increment were observed for patients positive for second-trimester sonographic markers (1.5%) and for the presence of fetal structural anomalies (1.3%). In contrast, the incremental yield was marginal in patients with fetus with increased nuchal translucency (0.5%). Conclusion The present study indicates that routine implementation of aCGH offers an incremental yield over conventional karyotype analysis, which is also present in cases with ‘milder’ indications, further supporting its use as a first-tier test. © 2015 John Wiley & Sons, Ltd.

Complex chromosomal rearrangements (CCRs) are balanced or unbalanced structural rearrangements involving 3 or more cytogenetic break events on 2 or more different chromosomes. Here, we report a 7-year-old girl referred to our unit because of mild dysmorphic facial features, mild learning difficulties together with very mild mental retardation. Standard cytogenetic banding analysis revealed a de novo CCR involving chromosomes 1, 2 and 18. Further molecular investigation with aCGH revealed a cryptic interstitial deletion of 2.7 Mb in 18q22.1, which does not elicit a significant clinical phenotype. FISH was performed to confirm both molecular and cytogenetic results.

Background Short arm deletions of the X-chromosome are challenging issues for genetic counseling due to their low penetrance in population. Female carriers of these deletions have milder phenotype than male ones, considering the intellectual ability and social skills, probably because of the X-chromosome inactivation phenomenon. Case report A female patient with a 10Mb distal Xp deletion and an Xq duplication, showing mild intellectual disability, is described in this report. While the deletion arose from a maternal pericentric inversion, the duplication was directly transmitted from the mother who is phenotypically normal. Conclusion This report underlines the usefulness of molecular cytogenetic technics in postnatal diagnosis.

Cantú syndrome is a very rare autosomal dominant disorder characterized by generalized congenital hypertrichosis, neonatal macrosomia, coarse face, cardiomegaly, and occasionally, skeletal abnormalities. The syndrome has been attributed to mutated ABCC9 or KCNJ8 genes. We present a 4-year-old girl with developmental delay, distinctive coarse facial features, and generalized hypertrichosis apparent since birth. The investigation revealed absent ovaries and a hypoplastic uterus which have not been previously described. Conventional karyotyping was normal. DNA sequencing analysis of the ABCC9 gene was performed, and a heterozygous point mutation c.3460C>T (p.Arg1154Trp) was revealed. This missense gain-of-function mutation was located in exon 27 of the ABCC9 gene and has been reported in patients with the full phenotype of Cantú syndrome. However, the absence of the ovaries could be an expansion of the phenotype and not attributed to mutations in other genes important for ovarian development. Unfortunately, it has not been proven so far if the ABCC9 gene is expressed in the ovarian tissue.

We report on a 27 month old boy presenting with psychomotor delay and dysmorphic features, mainly mild facial asymmetry, prominent cup-shaped ears, long eyelashes, open mouth appearance and slight abnormalities of the hands and feet. Array comparative genomic hybridization revealed a 393 kb microdeletion in 7p11.2. We discuss the possible involvement of CHCHD2, GBAS, MRPS17, SEPT14 and PSPH on our patient's phenotype. Additionally, we studied the expression of two other genes deleted in the patient, CCT6A and SUMF2, for which there is scarce data in the literature. Based on current knowledge and the de novo occurrence of this finding in our proband we presume that the aberration is likely to be pathogenic in our case. However, a single gene disorder, elsewhere in the genome or in this very region cannot be ruled out. Further elucidation of the properties of this chromosomal region, as well as of the role of the genes involved will be needed in order to draw safe conclusions regarding the association of the chromosomal deletion with the patient's features., Highlights • We report in detail the clinical and cytogenetic findings of a 27-month old male. • We compare our findings with current literature and online databases. • We discuss the possible involvement of certain genes in our patient’s phenotype.

Proximal 10q duplication is a well-defined but rare genetic syndrome. Duplication of proximal segments of the long arm of chromosome 10 results in a pattern of malformations, which are distinct from those of the more common distal 10q trisomy syndrome. The present study describes the case of a boy with phenotypic abnormalities (severe central hypotonia, mild ataxia, moderate developmental delay and mild dysmorphic features), due to duplication of chromosome region, 10q11.21→q11.22, which was characterized by the array-comparative genomic hybridization (CGH) technique. The phenotypic findings were compared with those in eight additional similar published cases. Major similarities have emerged, suggesting a likely minimal critical region. However, only detailed characterization of additional cases may provide firm conclusions.

Diabetes & Metabolism - In Press.Proof corrected by the author Available online since dimanche 12 juillet 2015

Twenty-nine as yet unreported ring chromosomes were characterized in detail by cytogenetic and molecular techniques. For FISH (fluorescence in situ hybridization) previously published high resolution approaches such as multicolor banding (MCB), subcentromere-specific multi-color-FISH (cenM-FISH) and two to three-color-FISH applying locus-specific probes were used. Overall, ring chromosome derived from chromosomes 4 (one case), 10 (one case), 13 (five cases), 14, (three cases), 18 (two cases), 21 (eight cases), 22 (three cases), X (five cases) and Y (one case) were studied. Eight cases were detected prenatally, eight due developmental delay and dysmorphic signs, and nine in connection with infertility and/or Turner syndrome. In general, this report together with data from the literature, supports the idea that ring chromosome patients fall into two groups: group one with (severe) clinical signs and symptoms due to the ring chromosome and group two with no obvious clinical problems apart from infertility.

To calculate the proportion of array comparative genomic hybridization (aCGH) pathogenic results, that would not be detectable by non-invasive prenatal screening (NIPS).This is a comparative study using data from 2779 fetuses, which underwent invasive prenatal diagnosis, and the samples were analyzed using aCGH. The simulated NIPS assay would test for trisomies 21, 18, 13, monosomy X, 47, XXX, 47, XYY, and 47, XXY. Indications for invasive testing were grouped into categories and the absolute, relative rates of pathogenic/likely pathogenic results of aCGH analysis that would not be detectable by NIPS were calculated.The expected rate of aCGH-detected abnormalities that would not be detectable by NIPS was 28.0% (95% CI 14.3-47.6) for nuchal translucency (NT) 95 to 99th centile; 14.3% (95% 5.0-34.6) for NT 99th centile; 34.2% (95% CI 21.1-50.1) for high-risk first-trimester results (regardless of NT); 52.4% (95% CI 32.4-71.7) for second-trimester markers; and 50.0% (95% CI 26.8-73.2) for advanced maternal age. The overall rate of aCGH pathogenic/likely pathogenic results was 5.0% and 44.0% (95% CI 36.0-52.2) of them would not be detected by NIPS.Approximately half of the abnormal aCGH results would not be detectable by standard NIPS assays, highlighting the necessity of pre-test counseling, and illustrating the limitations of NIPS. © 2017 John WileySons, Ltd.

Background FOXG1 gene mutations have been associated with the congenital variant of Rett syndrome (RTT) since the initial description of two patients in 2008. The on-going accumulation of clinical data suggests that the FOXG1-variant of RTT forms a distinguishable phenotype, consisting mainly of postnatal microcephaly, seizures, hypotonia, developmental delay and corpus callosum agenesis. Case presentation We report a 6-month-old female infant, born at 38 weeks of gestation after in vitro fertilization, who presented with feeding difficulties, irritability and developmental delay from the first months of life. Microcephaly with bitemporal narrowing, dyspraxia, poor eye contact and strabismus were also noted. At 10 months, the proband exhibited focal seizures and required valproic acid treatment. Array-Comparative Genomic Hybridization revealed a 4.09 Mb deletion in 14q12 region, encompassing the FOXG1 and NOVA1 genes. The proband presented similar feature with patients with 14q12 deletions except for dysgenesis of corpus callosum. Disruption of the NOVA1 gene which promotes the motor neurons apoptosis has not yet been linked to any human phenotypes and it is uncertain if it affects our patient’s phenotype. Conclusions Since our patient is the first reported case with deletion of both genes (FOXG1-NOVA1), thorough clinical follow up would further delineate the Congenital Rett-Variant phenotypes.

Two cases of liveborn unrelated children with developmental delay and overlapping unbalanced translocations der(8)t(8;16)(p23.2;q23.3) and der (8)t(8;16)(p23.1;q23.1), leading to partial monosomy 8p and partial trisomy 16q, are reported in the present study. The first patient was a 10-year-old boy with mild developmental delay and minor congenital anomalies (borderline microcephaly, clinodactyly, hypertelorism, epicanthus, mild systolic murmur and kidney reflux). The second patient was a 3 year-old girl with developmental delay, gross motor milestone delay and dysmorphic features. Array-comparative genomic hybridization analysis revealed that partial chromosome 8p monosomy extended from 8p23.2 to 8pter (4.8 Mb) in Patient 1 and from 8p23.1 to 8pter (9.5 Mb) in Patient 2, and partial chromosome 16 trisomy extended from 16q23.3 to 16qter (5.6 Mb) in Patient 1 and from 16q23.1 to 16qter (11.7 Mb) in Patient 2. The mechanism of appearance of the rearrangement in association with the genes involved and the architecture of the region is discussed.

Traditional approaches for the classification of Small Supernumerary Marker Chromosomes (sSMC), mostly based on FISH techniques, are time-consuming and not always sufficient to fully understand the true complexity of this class of rearrangements. We describe four supernumerary marker chromosomes that, after array-CGH, were interpreted rather differently in respect to the early classification made by conventional cytogenetics and FISH investigations, reporting two types of complex markers which DNA content was overlooked by conventional approaches: 1. the sSMC contains non-contiguous regions of the same chromosome and, 2. the sSMC, initially interpreted as a supernumerary del(15), turns out to be a derivative 15 to which the portion of another chromosome was attached. All are likely derived from partial trisomy rescue events, bringing further demonstration that germline chromosomal imbalances are submitted to intense reshuffling during the embryogenesis, leading to unexpected complexity and changing the present ideas on the composition of supernumerary marker chromosomes.

Polymorphisms of the cytotoxic T-lymphocyte antigen-4 gene (CTLA-4) have been associated with autoimmune diseases and it has recently been reported that donor genotypes correlate with the outcome of allogeneic hematopoietic stem cell transplantation in leukemia patients. With the aim of confirming this finding in thalassemia patients, we investigated the influence of genotype distribution of 3 CTLA-4 gene polymorphisms in 72 thalassemia patients and their unrelated donors. A significant association was observed for recipient CT60-AA genotype and onset of grade II–IV (63.2% vs 24.5%; p = 0.001) and grade III–IV (36.4% vs 7.6%; p = 0.005) acute graft-versus-host disease (aGVHD). The same association was observed for the 88-base-pair allele of the CTLA-4 (AT)n polymorphism, which was determined to be in complete linkage disequilibrium with the CT60 A allele. Multinomial Cox regression demonstrated that this association was independent of CT60 donor genotypes or other risk factors (p = 0.016; hazard ratio = 2.8). Our data confirm that the genetic variability in CTLA-4 is an important prognostic factor for aGVHD and suggest that some of the risk factors for this complication are generated by recipient cells that persist after the myeloablative conditioning regimen.

Rare intrachromosomal triplications producing partial tetrasomies have been reported for a number of chromosomes. A detailed molecular characterization, necessary to define the mechanism of their formation, has so far been lacking. We report on the detailed clinical, cytogenetic, and molecular characterization of two triplications, one de novo involving chromosome 18q, the other familial on chromosome Xp. The clinical phenotype of the patient with 18q triplication, very likely due to overexpression of one or more of the genes in the region, consists mainly of facial dysmorphisms and developmental delay. The familial Xp triplication does not cause an increase in the number of copies of any gene and is almost certainly a polymorphism. The rearrangements are actually complex duplications/triplications. In both patients, their proximal breakpoints are located within complex segmental duplications, one containing the VCX gene cluster on chromosome Xp, the other the TCEB3 genes on chromosome 18q. A proximal duplicated region is also present in both patients. All junctions we analyzed were formed by non-homologous end joining (NHEJ). The structural features shared between our patients suggest the involvement of a common mechanism in the genesis of interstitial intrachromosomal triplications. © 2011 Wiley Periodicals, Inc.