Further delineation of the rare GDACCF (global developmental delay, absent or hypoplastic corpus callosum, dysmorphic facies syndrome): genotype and phenotype of 22 patients with ZNF148 mutations.

BACKGROUND: Pathogenic variants in the zinc finger protein coding genes are rare causes of intellectual disability and congenital malformations. Mutations in the ZNF148 gene causing GDACCF syndrome (global developmental delay, absent or hypoplastic corpus callosum, dysmorphic facies; MIM #617260) have been reported in five individuals so far. METHODS: As a result of an international collaboration using GeneMatcher Phenome Central Repository and personal communications, here we describe the clinical and molecular genetic characteristics of 22 previously unreported individuals. RESULTS: The core clinical phenotype is characterised by developmental delay particularly in the domain of speech development, postnatal growth retardation, microcephaly and facial dysmorphism. Corpus callosum abnormalities appear less frequently than suggested by previous observations. The identified mutations concerned nonsense or frameshift variants that were mainly located in the last exon of the ZNF148 gene. Heterozygous deletion including the entire ZNF148 gene was found in only one case. Most mutations occurred de novo, but were inherited from an affected parent in two families. CONCLUSION: The GDACCF syndrome is clinically diverse, and a genotype-first approach, that is, exome sequencing is recommended for establishing a genetic diagnosis rather than a phenotype-first approach. However, the syndrome may be suspected based on some recurrent, recognisable features. Corpus callosum anomalies were not as constant as previously suggested, we therefore recommend to replace the term 'GDACCF syndrome' with 'ZNF148-related neurodevelopmental disorder'.

Bi-allelic loss-of-function variants in KIF21A cause severe fetal akinesia with arthrogryposis multiplex.

BACKGROUND: Fetal akinesia (FA) results in variable clinical presentations and has been associated with more than 166 different disease loci. However, the underlying molecular cause remains unclear in many individuals. We aimed to further define the set of genes involved. METHODS: We performed in-depth clinical characterisation and exome sequencing on a cohort of 23 FA index cases sharing arthrogryposis as a common feature. RESULTS: We identified likely pathogenic or pathogenic variants in 12 different established disease genes explaining the disease phenotype in 13 index cases and report 12 novel variants. In the unsolved families, a search for recessive-type variants affecting the same gene was performed; and in five affected fetuses of two unrelated families, a homozygous loss-of-function variant in the kinesin family member 21A gene (KIF21A) was found. CONCLUSION: Our study underlines the broad locus heterogeneity of FA with well-established and atypical genotype-phenotype associations. We describe KIF21A as a new factor implicated in the pathogenesis of severe neurogenic FA sequence with arthrogryposis of multiple joints, pulmonary hypoplasia and facial dysmorphisms. This hypothesis is further corroborated by a recent report on overlapping phenotypes observed in Kif21a null piglets.

A single center experience of prenatal parent-fetus trio exome sequencing for pregnancies with congenital anomalies.

OBJECTIVES: To examine the diagnostic yield of trio exome sequencing in fetuses with multiple structural defects with no pathogenic findings in cytogenetic and microarray analyses. METHODS: We recruited 51 fetuses with two or more defects, non-immune fetal hydrops or fetal akinesia deformation syndrome|or fetal akinesia deformation sequence (FADS). Trio exome sequencing was performed on DNA from chorionic villi samples and parental blood. Detection of genomic variation and prioritization of clinically relevant variants was performed according to in-house standard operating procedures. RESULTS: Median maternal and gestational age was 32.0 years and 21.0 weeks, respectively. Forty-three (84.3%) fetuses had two or more affected organ systems. The remaining fetuses had isolated fetal hydrops or FADS. In total, the exome analysis established the genetic cause for the clinical abnormalities in 22 (43.1%, 95% CI 29.4%-57.8%) pregnancies. CONCLUSIONS: In fetuses with multiple defects, hydrops or FADS and normal standard genetic results, trio exome sequencing has the potential to identify genetic anomalies in more than 40% of cases.

Pre- and postnatal findings in a patient with a recombinant chromosome rec(8)(qter→q21.11::p23.3→qter) due to a paternal pericentric inversion inv(8)(p23.3q21.11) and review of the literature.

Recombinant chromosome 8 (Rec8) syndrome (San Luis Valley [SLV] syndrome; OMIM #179613) is a rare chromosome disorder associated with intellectual disability, congenital heart defects, variable skeletal and urogenital anomalies, and dysmorphic features. It is characterized by a partial terminal deletion of 8p and a partial terminal duplication of 8q, which is usually due to meiotic recombination of a pericentric inversion of chromosome 8 of a healthy carrier parent. There are only few reports of cases with breakpoints defined at the molecular level by molecular karyotyping. We report on a case of Rec8 syndrome with previously unreported breakpoints in a male fetus with intrauterine growth restriction, hypogenesis of the corpus callosum, bilateral cleft lip/palate, and congenital heart defect. Cytogenetic analysis revealed a recombinant chromosome 8 [46,XY,rec(8)(qter→q21.11::p23.3→qter)] secondary to a paternal pericentric inversion [46,XY,inv(8)(p23.3q21.11)]. Molecular karyotyping correspondingly showed a terminal copy number loss of 1.4 Mb (arr[hg19] 8p23.3(158048_1514749)×1) and a terminal copy number gain of chromosome band 8q21.11q24.3 of 69.8 Mb (arr[hg19] 8q21.11q24.3(76477367_146295771)×3). To our knowledge, this is the fourth reported case diagnosed prenatally. We describe the postnatal clinical course of the male newborn. Furthermore, we review and compare the phenotypic features and breakpoints of 74 reported Rec8/SLV cases.

Investigating the effects of additional truncating variants in DNA-repair genes on breast cancer risk in BRCA1-positive women.

BACKGROUND: Inherited pathogenic variants in BRCA1 and BRCA2 are the most common causes of hereditary breast and ovarian cancer (HBOC). The risk of developing breast cancer by age 80 in women carrying a BRCA1 pathogenic variant is 72%. The lifetime risk varies between families and even within affected individuals of the same family. The cause of this variability is largely unknown, but it is hypothesized that additional genetic factors contribute to differences in age at onset (AAO). Here we investigated whether truncating and rare missense variants in genes of different DNA-repair pathways contribute to this phenomenon. METHODS: We used extreme phenotype sampling to recruit 133 BRCA1-positive patients with either early breast cancer onset, below 35 (early AAO cohort) or cancer-free by age 60 (controls). Next Generation Sequencing (NGS) was used to screen for variants in 311 genes involved in different DNA-repair pathways. RESULTS: Patients with an early AAO (73 women) had developed breast cancer at a median age of 27 years (interquartile range (IQR); 25.00-27.00 years). A total of 3703 variants were detected in all patients and 43 of those (1.2%) were truncating variants. The truncating variants were found in 26 women of the early AAO group (35.6%; 95%-CI 24.7 - 47.7%) compared to 16 women of controls (26.7%; 95%-CI 16.1 to 39.7%). When adjusted for environmental factors and family history, the odds ratio indicated an increased breast cancer risk for those carrying an additional truncating DNA-repair variant to BRCA1 mutation (OR: 3.1; 95%-CI 0.92 to 11.5; p-value = 0.07), although it did not reach the conventionally acceptable significance level of 0.05. CONCLUSIONS: To our knowledge this is the first time that the combined effect of truncating variants in DNA-repair genes on AAO in patients with hereditary breast cancer is investigated. Our results indicate that co-occurring truncating variants might be associated with an earlier onset of breast cancer in BRCA1-positive patients. Larger cohorts are needed to confirm these results.

HBOC multi-gene panel testing: comparison of two sequencing centers.

Multi-gene panels are used to identify genetic causes of hereditary breast and ovarian cancer (HBOC) in large patient cohorts. This study compares the diagnostic workflow in two centers and gives valuable insights into different next-generation sequencing (NGS) strategies. Moreover, we present data from 620 patients sequenced at both centers. Both sequencing centers are part of the German consortium for hereditary breast and ovarian cancer (GC-HBOC). All 620 patients included in this study were selected following standard BRCA1/2 testing guidelines. A set of 10 sequenced genes was analyzed per patient. Twelve samples were exchanged and sequenced at both centers. NGS results were highly concordant in 12 exchanged samples (205/206 variants = 99.51 %). One non-pathogenic variant was missed at center B due to a sequencing gap (no technical coverage). The custom enrichment at center B was optimized during this study; for example, the average number of missing bases was reduced by a factor of four (vers. 1: 1939.41, vers. 4: 506.01 bp). There were no sequencing gaps at center A, but four CCDS exons were not included in the enrichment. Pathogenic mutations were found in 12.10 % (75/620) of all patients: 4.84 % (30/620) in BRCA1, 4.35 % in BRCA2 (27/620), 0.97 % in CHEK2 (6/620), 0.65 % in ATM (4/620), 0.48 % in CDH1 (3/620), 0.32 % in PALB2 (2/620), 0.32 % in NBN (2/620), and 0.16 % in TP53 (1/620). NGS diagnostics for HBOC-related genes is robust, cost effective, and the method of choice for genetic testing in large cohorts. Adding 8 genes to standard BRCA1- and BRCA2-testing increased the mutation detection rate by one-third.

Interstitial 1p32.1p32.3 deletion in a patient with multiple congenital anomalies.

Interstitial deletions encompassing chromosome bands 1p32.1p32.3 are rare. Only nine unrelated patients with partially overlapping 1p32.1p32.3 deletions of variable size and position have been reported to date. We report on a 17-month-old boy with choanal atresia, hearing loss, urogenital anomalies, and microcephaly in whom an interstitial de novo deletion of 6.4 Mb was detected in 1p32.1p32.3 (genomic position chr1:54,668,618-61,113,264 according to GRCh37/hg19). The deleted region harbors 31 RefSeq genes. Notable genes in the region are PCSK9, haploinsufficiency of which caused low LDL cholesterol plasma levels in the patient, and DAB1, which is a candidate gene for cognitive deficits, microcephaly, and cerebral abnormalities such as ventriculomegaly and agenesis of the corpus callosum. Choanal atresia, microcephaly, and severe hearing loss were previously not known to be associated with 1p32 deletions. Our reported patient thus broadens the spectrum of clinical findings in this chromosome region and further facilitates genotype-phenotype correlations. Additional patients with overlapping deletions and/or point mutations in genes of this region need to be identified to elucidate the role of individual genes for the complex clinical manifestations.

Interstitial duplication of chromosome region 1q25.1q25.3: report of a patient with mild cognitive deficits, tall stature and facial dysmorphisms.

Isolated interstitial duplications of chromosome band 1q25 are apparently very rare; no patients with detailed molecular and clinical characterization of duplications restricted to this region have been published to date. We report on a 9-year-old girl with mild cognitive deficits, tall stature, macrocephaly and discrete dysmorphic features in whom a de novo interstitial 7.5 Mb duplication of 1q25.1q25.3 was detected by SNP array analysis (arr[hg19] 1q25.1q25.3(173,925,505-181,381,242)x3 dn). The duplicated region was inversely inserted into chromosome band 1q42.2: 46,XX,der(1)(pter→q42.2::q25.3→q25.1::q42.2→qter). Overexpression of one or several of the 87 genes in the duplicated interval was presumably the major causative factor for the clinical manifestations. Reports of additional patients with overlapping duplications will be needed to establish detailed karyotype-phenotype correlations and to gain a better understanding of the underlying pathomechanisms.

A further case of AFG2B-related neurodevelopmental disorder with hearing loss and microcephaly allows further clarification of pathogenicity of the variant c.1313T>C, p.(Leu438Pro).

BACKGROUND: Bi-allelic variants in AFG2B (previously known as SPATA5L1) have recently been associated with a neurodevelopmental disorder with hearing loss and spasticity, as well as isolated hearing loss. We report on a 6 1/2-year-old girl with a history of global developmental delay, subsequent intellectual disability without relevant language acquisition, sensorineural hearing loss, muscular hypotonia and microcephaly. METHODS: We performed trio exome sequencing on the patient and her parents. RESULTS: Trio exome sequencing revealed likely pathogenic compound heterozygous missense variants in AFG2B [c.527G>T, p.(Gly176Val) and c.1313T>C, p.(Leu438Pro)] in the patient. CONCLUSION: Of note, the change c.1313T>C, p.(Leu438Pro) has been observed in a previously published patient as part of a complex disease allele along with a second homozygous missense change, so the exact contribution of the two alterations to this patient's disease had initially remained unclear. Our results support the pathogenic relevance of the c.1313T>C, p.(Leu438Pro) allele while providing detailed insights into the disease manifestation of a further patient.

12q24.33 deletion: report of a patient with intellectual disability and review of the literature.

Deletions of chromosome band 12q24.33 are rare. We report on a 17-year-old male patient with intellectual disability but no major malformations or dysmorphic features in whom a de novo interstitial 660 kb deletion in 12q24.33 was detected by SNP array analysis. This deletion was secondary to a translocation t(12;14)(q24.3;q13)dn that also led to a small deletion in 14q21.1 and a small duplication in 2p23.1. The deletion overlaps with two previously published larger deletions in patients who suffered from intellectual disability, obesity, and polycystic kidney disease, indicating that haploinsufficiency of one or several of the genes in the deleted interval of the patient reported here causes intellectual deficits, but not obesity or renal problems. The 14 RefSeq genes that are harbored by this deletion include P2RX2, which had previously been proposed as a candidate gene for intellectual disability. Thus, the patient reported here broadens our knowledge of the phenotypic consequences of deletions in 12q24.33 and facilitates genotype-phenotype correlations for chromosome aberrations of this region.

A longitudinal study of cerebral blood flow over the first 30 months.

To investigate prospectively the development of cerebral perfusion during infancy, serial quantitative measurements of cerebral blood flow (CBF) volume were performed in two healthy children from birth up to the age of 30 mo. A total of 28 CBF volume measurements were done in either of the children. Absolute flows were measured in the internal carotid and vertebral arteries on both sides. Blood flow was calculated as the product of angle-corrected time-averaged flow velocity and the cross-sectional area of the vessel. Starting from 67 and 80 mL/min, respectively, at birth an almost 10-fold increase of CBF volume was observed in both children during the examination period. Half of this rise occurred during the first 6 mo, probably reflecting the steep metabolic incline during this period of synaptogenesis. The continuous increase in CBF volume after the sixth month of life mainly corresponds to brain growth. Estimated CBF (based on estimated brain weights) increased from 21 and 23 mL 100 g(-1) min(-1), respectively, after birth to 46 and 53 mL 100 g(-1) min(-1), respectively, during the first 6 mo of life in both children, remaining stable thereafter. This study is the first to provide longitudinal data of CBF during the first 30 mo after birth.

Novel HIVEP2 Variants in Patients with Intellectual Disability.

Intellectual disability (ID) occurs in approximately 1% of the population. Over the last years, broad sequencing approaches such as whole exome sequencing (WES) substantially contributed to the definition of the molecular defects underlying nonsyndromic ID. Pathogenic variants in HIVEP2, which encodes the human immunodeficiency virus type I enhancer binding protein 2, have recently been reported as a cause of ID, developmental delay, behavioral disorders, and dysmorphic features. HIVEP2 serves as a transcriptional factor regulating NF-ĸB and diverse genes that are essential in neural development. To date, only 8 patients with pathogenic de novo nonsense or frameshift variants and 1 patient with a pathogenic missense variant in HIVEP2 have been reported. By WES, we identified 2 novel truncating HIVEP2 variants, c.6609_6616delTGAGGGTC (p.Glu2204*) and c.6667C>T (p.Arg2223*), in 2 young adults presenting with developmental delay and mild ID without any dysmorphic features, systemic malformations, or behavioral issues.

Prenatal multicystic encephalomalacia due to anomaly of the aortic arch.

Multicystic encephalomalacia (ME) usually results from severe hypoxic-ischemic brain damage occurring during the late third trimester of gestation and birth. We report on a case of congenital ME due to a congenital anomaly of the aortic origin of brachiocephalic vessels resulting in subclavian steal syndrome. A 5-day-old term neonate presented with microcephaly and overlapping cranial sutures. Both arms were developed normally. Magnetic resonance imaging of the brain showed extensive bilateral supratentorial ME. Color duplex sonography of the aortic arch and the intracranial and extracranial vessels revealed a stenosis at the origin of the left common carotid artery and atresia of the origin of the left subclavian artery resulting in left-sided subclavian steal syndrome and retrograde perfusion of the basilar artery. Total cerebral blood flow volume was reduced to 22 mL/min. Severely reduced cerebral blood flow volume resulted from left carotid artery stenosis and atresia of the origin of the left subclavian artery with consecutive subclavian steal. Infratentorial brain structures and the left arm remained intact, but supratentorial brain structures were severely affected with ME.

Cerebral blood flow volume measurements with ultrasound: Interobserver reproducibility in preterm and term neonates.

Cerebral blood flow (CBF) volume can be measured quantitatively by colour duplex sonography. To test the reliability of CBF volume measurements in newborns, two "blinded" examiners performed a prospective test-retest study in 32 neonates (postmenstrual age 32 to 42 weeks). Measurements were done in the internal carotid and vertebral arteries. Intravascular flow volumes (FV) were calculated as the product of angle-corrected time-averaged flow velocity and the cross-sectional area of the vessel. The CBF volumes measured by the two examiners were very close (mean +/- SD, 62.6 +/- 20.6 vs. 62.1 +/- 21.2 mL/min, NS; coefficient of variation, 6.3%; intraclass correlation coefficient, 0.98). The 95% limits of agreement, according to Bland and Altman, ranged from -7.3 to +8.4 mL/min. In comparison with other test-retest studies, the reproducibility of quantitative CBF measurements reported here is among the best ever found. We conclude that CBF volume can be measured reliably even in preterm neonates.

Next-generation sequencing in X-linked intellectual disability.

X-linked intellectual disability (XLID) is a genetically heterogeneous disorder with more than 100 genes known to date. Most genes are responsible for a small proportion of patients only, which has hitherto hampered the systematic screening of large patient cohorts. We performed targeted enrichment and next-generation sequencing of 107 XLID genes in a cohort of 150 male patients. Hundred patients had sporadic intellectual disability, and 50 patients had a family history suggestive of XLID. We also analysed a sporadic female patient with severe ID and epilepsy because she had strongly skewed X-inactivation. Target enrichment and high parallel sequencing allowed a diagnostic coverage of >10 reads for ~96% of all coding bases of the XLID genes at a mean coverage of 124 reads. We found 18 pathogenic variants in 13 XLID genes (AP1S2, ATRX, CUL4B, DLG3, IQSEC2, KDM5C, MED12, OPHN1, SLC9A6, SMC1A, UBE2A, UPF3B and ZDHHC9) among the 150 male patients. Thirteen pathogenic variants were present in the group of 50 familial patients (26%), and 5 pathogenic variants among the 100 sporadic patients (5%). Systematic gene dosage analysis for low coverage exons detected one pathogenic hemizygous deletion. An IQSEC2 nonsense variant was detected in the female ID patient, providing further evidence for a role of this gene in encephalopathy in females. Skewed X-inactivation was more frequently observed in mothers with pathogenic variants compared with those without known X-linked defects. The mutation rate in the cohort of sporadic patients corroborates previous estimates of 5-10% for X-chromosomal defects in male ID patients.

Postnatal decrease in substantia nigra echogenicity. Implications for the pathogenesis of Parkinson's disease.

Increased echogenicity of the substantia nigra (SN) on transcranial ultrasonography (TCS) is a typical sign in Parkinson's disease (PD). Detected in healthy adults it is assumed to represent a risk factor for nigral injury. We studied at which time point of brain maturation increased signal intensity may occur by performing TCS scans in 109 newborns and children aged 0-192 months. While newborns regularly exhibit SN hyperechogenicity, this echofeature decreases substantially during the first years of life. As SN echogenicity is related to the tissue iron content in adults our findings suggest a failure in SN iron metabolism in some children with increased echogenicity during development which can be disclosed by TCS.

The development of haemodynamics in the extracranial cerebral arteries of healthy preterm and term neonates.

To investigate the development of cerebral haemodynamics in healthy preterm and term newborns, a prospective colour duplex sonography study was performed in 113 neonates at 32 to 42 weeks of postmenstrual age. In the extracranial internal carotid arteries (ICAs) and vertebral arteries (VAs), luminal diameters and angle-corrected flow velocities were measured. Flow volumes and waveform parameters were calculated. There were no side-to-side or gender-related differences for any of the parameters measured. A marked increase of luminal diameters, end-diastolic and time-averaged flow velocities and flow volumes with postmenstrual age was found in both ICA and VA (p

The effect of vasospasm on cerebral perfusion: a colour duplex study of the extra- and intracranial cerebral arteries.

To assess whether middle cerebral artery (MCA) vasospasm reduces the flow volume in the corresponding extracranial internal carotid artery (ICA) or global cerebral blood flow volume (CBFV) in subarachnoid haemorrhage (SAH) patients, a colour duplex ultrasound study of the intra- and extracranial cerebral arteries was performed. MCA vasospasm was defined as a time-averaged maximum flow velocity (TAMX) exceeding 120 cm/s. ICA flow volumes and CBFV, were compared in each patient at maximum TAMX recorded in one MCA ("maximum-vasospasm") and when TAMX in the same vessel was closest to mean reference values ("no-vasospasm"). Additionally, the CBFV course during the first 3 weeks after SAH was evaluated longitudinally. Data from age- and gender-matched healthy test persons served as control. In 28 patients with MCA vasospasm, 337 measurements were completed. Global CBFV was significantly reduced starting from day 3 after SAH. ICA flow volumes and CBFV were not different when comparing at "maximum-vasospasm" and "no-vasospasm". Compared with the control group, both were lower at either condition. Thus, in SAH patients, vasospasm even severe, in general does not further diminish ICA flow volumes and global CBFV, which are reduced already before the onset of vasospasm.

Development of cerebral blood flow volume in preterm neonates during the first two weeks of life.

To investigate the postnatal development of cerebral perfusion in preterm neonates with normal brains over the first 2 wk of life, a prospective longitudinal study was designed. Quantitative measurement of cerebral blood flow (CBF) volume was performed using ultrasound flowmetry of the extracranial, brain-feeding arteries in 32 preterm infants of 28-35 wk gestational age. Measurements were done in the internal carotid and vertebral arteries of both sides on d 1, 2, 3, 7, and 14 after birth. A 10.0-MHz linear transducer of a computed sonography system (Acuson 128/XP10) was used. Intravascular flow volumes were calculated as the product of angle-corrected time-averaged flow velocity and the cross-sectional area of the vessel. Mean CBF volume increased markedly over the first 2 wk. One-third of this rise already occurred from the first to the second postnatal day, thereafter there was a continuous increase from d 2 to d 14 of life. Whereas the absolute level of CBF volume was primarily determined by postmenstrual age, the pattern of postnatal changes in CBF volume was found to be independent of gestational age. Arterial carbon dioxide tension, mean arterial blood pressure, and hematocrit had no influence on the development of CBF volume. The pronounced increase of CBF volume from d 1 to d 2 is likely to represent a normal adaptive response of the cerebral circulation to postnatal life. The data presented here may serve as the basis for further studies to investigate whether deviations from this adaptive response are associated with an increased risk of brain injury.