Whole-genome sequencing reveals individual and cohort level insights into chromosome 9p syndromes

Previous genomic efforts on chromosome 9p deletion and duplication syndromes have utilized low resolution strategies (i.e., karyotypes, chromosome microarrays). We present the first large-scale whole-genome sequencing (WGS) study of 100 individuals from families with 9p-related syndromes including 85 unrelated probands through the 9P-ARCH (Advanced Research in Chromosomal Health: Genomic, Phenotypic, and Functional Aspects of 9p-Related syndromes) research network. We analyzed the genomic architecture of these syndromes, highlighting fundamental features and their commonalities and differences across individuals. This work includes a machine-learning model that predicts 9p deletion syndrome from gene copy number estimates using WGS data. Two Late Replicating Regions (LRR1 [a previously un-named human fragile site], LRR2) were identified that contain most structural variant breakpoints in 9p deletion syndrome pointing to replication-based issues in structural variant formation. Furthermore, we show the utility of using WGS information to obtain a comprehensive understanding of 9p-related variation in an individual with complex structural variation where chromothripsis is the likely mechanism. Genes on 9p were prioritized based on statistical assessment of human genomic variation. Furthermore, through application of spatial transcriptomics to embryonic mouse tissue we examined 9p-gene expression in craniofacial and brain development. Through these strategies, we identified 24 important genes for the majority (83%) of individuals with 9p deletion syndrome including AK3, BRD10, CD274, CDC37L1, DMRT1, DMRT2, DMRT3, DOCK8, GLIS3, JAK2, KANK1, KDM4C, PLPP6, PTPRD, PUM3, RANBP6, RCL1, RFX3, RIC1, SLC1A1, SMARCA2, UHRF2, VLDLR, and ZNG1A. Two genes (AK3, ZNG1A) are involved in mitochondrial function and testing of the mitochondrial genome revealed excess copy number in individuals with 9p deletion syndrome. This study presents the most comprehensive genomic analysis of 9p-related syndromes to date, with plans for further expansion through our 9P-ARCH research network.

Background 18p deletion (18p-) syndrome is a rare chromosomal abnormality with a wide range of phenotypes. Its main clinical features are short stature, intellectual disability, and facial dysmorphism, which are rarely accompanied by autoimmune thyroid disease (ATD) or pituitary abnormalities. Herein, we report the first Chinese patient with a de novo 18p deletion who presented with ATD. Case presentation: A 24-year-old female patient presented with severe ptosis, intellectual disability, hypothyroidism associated with Hashimoto’s thyroiditis, and a non-functional pituitary adenoma. Deletion of the short arm of chromosome 18 was detected in a G-banded karyotyping (46, XX, del [18] [p11.1]). Chromosomal microarray analysis revealed a 14.9Mb deletion in chromosome 18p11.32p11.21, defined as arr[GRCh38]18p11.32p11.21(136227–15079295)x1. The literature review indicated that patients with 18p- syndrome presenting with ATD were mainly female with early disease onset (mean age: 15 years). Conclusions 18p- syndrome is associated with ATD and pituitary abnormalities. Therefore, examining the endocrine system and detecting defective genes in the 18p breakpoint region are crucial in predicting prognosis.

Can Whole Genome and Whole Transcriptome Sequencing Replace Standard Procedures in CLL Diagnostics?

The chromosome 18p deletion (18p-) syndrome or monosomy of 18p is a rare chromosome abnormality, considered a contiguous gene deletion syndrome resulting from the deletion of a portion or most of the whole short arm of chromosome 18. Therefore, it can present a spectrum of phenotypes associated with different prognostic outcomes. Understanding the clinical variability of this condition is important once the fertility is preserved, impacting genetic counseling and reproductive outcomes. The aim of this article is to report a case of familial 18p deletion syndrome and its striking phenotypic variability within the same family. A male stillborn presenting alobar holoprosencephaly and his mother who presented with a single central incisor came to our attention for genetic investigation. Karyotype analysis and Fluorescent In Situ Hybridization (FISH) from a cordocentesis blood sample of the male stillborn was performed. Parents’ cytogenetic analyses were obtained through peripheral blood cultures. Chromosomes were analyzed after GTG banding. FISH technique was carried out on both the proband's and maternal samples using WCP18 (whole chromosome 18) specific probes, according to the manufacturer's protocols. The stillborn karyotype and FISH analysis revealed a deletion characterized by 46, XY del(18)(p11.1→pter).ish del(18)(p11.1→pter)(wcp18-). His mother showed the same deletion in 45% of the analyzed cells revealing a rare structural mosaicism. The striking phenotypic variability encountered in this family could be attributed to a genetic combination of the deleted segment in the proband; and the presence of a mosaic normal karyotype may very well attenuate the mother’s phenotypic presentation. The origin of an abnormally structural chromosome in mosaic possibly originated from a post-zygotic cell division event during the embryonic development of the mother. The consequences on the family offsprings of such rare cytogenetic event impacts greatly the family genetic counseling

Periventricular heterotopia (PH) is a malformation of cortical development characterized by the ectopic localization of neuronal nodules along the lateral ventricle. Mutations in X-linked filamin A gene are the most common cause of PH, although a rarer autosomal recessive form of PH with microcephaly due to ARFGEF2 mutations has been described [Sheen et al., 2001]. Affected individuals generally are of normal intelligence and most often present with adolescent onset seizures. The 1p36 deletion syndrome is associated with multiple congenital anomalies caused by haploinsufficiency of numerous contiguous genes. This deletion produces specific physical characteristics such as distinctive facial anomalies (pointed chin, flat nose, low set ears) and cardiovascular malformations (atrial septal defect, patent ductus arteriosus, tetralogy of Fallot). Central nervous system (CNS) defects include mental retardation, cranial nerve abnormalities (VI nerve palsies, optic disc anomalies, sensorineural hearing loss), neonatal hypotonia, cortical dysplasia, and seizures [Heilstedt et al., 2003; Kurosawa et al., 2005; Battaglia, 2005]. A reduction in the KCNAB2 potassium channel betasubunit has been hypothesized to be responsible for the seizures [Hirose et al., 2002]. Affected individuals can display outbursts, tendencies to strike people, and self-injurious behavior, as well as autistic-like behaviors [Slavotinek et al., 1999]. Previous neuroimaging and postmortem studies on individuals with 1p36 deletions have revealed mild CNS structural abnormalities. Deletions involving the most distal p-terminus (D1S508, 1p36.23-> 1pter) have only been associated with microcephaly, mild ventricular asymmetry, and ventricular enlargement [Kurosawa et al., 2005; Slavotinek et al., 1999]. An interstitial deletion (1p36.1->1p36.2) was suggested as causal for the development of neuroblastoma in a single case report [Keppler-Noreuil et al., 1995]. Finally, a series of three patients harboring 1p36.22->1pter deletions was reported to have hydrocephalus by cranial ultrasound but no mention of PH [Keppler-Noreuil et al., 1995]. To date, there have been no reported associations of PH with chromosome 1p36 deletions. Here, we describe the first case describing PH in an individual with a 1p36.22-> 1pter deletion. This study was approved by the IRB at the respective institutions in accordance with NIH. Informed consent was obtained from the participating subject’s parents. Genomic DNA was extracted from peripheral whole blood lymphocytes using standard blood DNA isolation techniques (Qiagen Inc., Valencia, CA). Metaphase chromosome analysis of lymphocytes was performed according to standard protocols. Initial routine karyotyping on the child was read as normal, although deletions on 1p36 are commonly missed due to the Giemsa-negative/poor staining in this region. Given the numerous clinical features seen in this subject, FISH analysis utilizing 41 subtelomere probes was performed (Genzyme laboratories (Hawthorne, NY), using Vysis probes (Downers Grove, IL). Results were confirmed with a chromosome 1p subtelomere probe (1pSUBTEL; Vysis) and the D1Z2 midi-satellite probe with repeats in band 1p36 (Oncor). The D1Z2 probe is used for confirmationof a commondeletion interval (1p36.3). A chromosome 1 centromere probe (D1Z5; Vysis)

Genomic and transcriptomic somatic alterations of hepatocellular carcinoma in non-cirrhotic livers

To analyze ultrasonographic finding in fetuses with Wolf-Hirschhorn syndrome (WHS) and refine the critical region on chromosome 4p16.3 for WHS-associated fetal growth retardation (FGR). In total 2262 fetuses with abnormal ultrasonographic findings who underwent prenatal karyotyping and chromosomal microarray analysis were reviewed. WHS-associated 4p deletions detected in these fetuses were compared, and prenatal ultrasound findings in such fetuses were summarized. Meanwhile, WHS cases with prenatal ultrasound findings and isolated 4p deletions in previous studies were included for further analysis. An analysis of smallest region of overlap (SRO) among discrepant 4p deletions in these cases above was performed to define a critical region for FGR. 4p deletions were detected in 10 of the 2262 fetuses and 5.0% of the 202 fetuses with FGR. Combined with 80 WHS cases from previous studies, the most common prenatal ultrasound finding was FGR, which yielded a frequency of 76.7%. In addition, a SRO spanning approximately 419 kb (genomic position: 1.32-1.74 Mb) on chromosome 4p16.3 was discovered by comparing the unusual 4p deletions among the 10 fetuses. The region contained seven protein-coding genes, including TACC3, SLBP, TMEM129, FAM53A, MAEA, UVSSA and CRIPAK. For fetuses with WHS, the most common prenatal ultrasound phenotype was FGR. A region between 1.32 Mb to 1.74 Mb from the telomere on chromosome 4p16.3 is critical for WHS-associated FGR, for which TACC3 and SLBP are the candidate genes.

5090 Background: We investigated whether deletion of chromosome 9p in clear cell renal cell carcinoma (ccRCC) predicts worse disease-specific (DSS) and recurrence-free survival (RFS), and if it is associated with worse prognosis in tumors < 4 cm. Methods: 316 patients undergoing nephrectomy prior to 2001 were included on a tissue microarray in whom FISH analysis using the LSI p16/CEP 9 Dual Color Probe was performed to assess chromosome 9p deletion status. An additional 389 patients undergoing nephrectomy after 2001 had 9p status determined by standard cytogenetics. Tumor grade, stage, size, 9p status, nodal involvement, and the presence of metastasis were recorded. Disease-specific and recurrence-free survival were determined, and independence was assessed using Cox proportional hazards models. Results: 9p deletions were detected in 14% of tumors. 54% of 9p-deleted tumors were high grade (G3–4) vs. 38% without 9p deletions, and 60% of 9p-deleted tumors were T3–4 vs 38% without 9p deletions (p < 0.01). 55% of those with 9p deletions had positive nodes or metastases vs. 34% of those without 9p deletions (p < 0.01). Median DSS for those with and without 9p deletions was 80 months and 37 months, respectively (p < 0.01). In localized disease, median RFS for those with 9p deletions was 53 months and was not reached in those without 9p deletions (p<0.01). In 188 patients presenting with localized RCC < 4 cm, loss of 9p occurred in 3/7 (42.9%) of patients with post-nephrectomy recurrence vs. 13/168 (7.2%) of patients without disease recurrence (p = 0.001). DSS for patients with 9p deletion in tumors < 4 cm was significantly worse than DSS in those without 9p deletions (HR 6.18; p = 0.02), and an independent effect on RFS was seen for 9p deletions in localized RCC (HR 2.3, p < 0.01). 9p status was not a significant predictor in metastatic RCC. Conclusions: Deletion of chromosome 9p in ccRCC occurs in 14% of patients and is associated with higher grade and T stage, presence of nodal and distant disease, worse prognosis, and in patients with small NOMO tumors, 9p deletions but not tumor size was independently associated with RFS. Identifying high risk patients with 9p deletions will allow better risk stratification for surveillance protocols and for adjuvant trials. No significant financial relationships to disclose.

Smith-Magenis syndrome (SMS) is a clinically recognizable contiguous gene syndrome ascribed to an interstitial deletion in chromosome 17p11.2. Seventy percent of SMS patients have a common deletion interval spanning 3.5 megabases (Mb). Clinical features of SMS include characteristic mild dysmorphic features, ocular anomalies, short stature, brachydactyly, and hypotonia. SMS patients have a unique neurobehavioral phenotype that includes intellectual disability, self-injurious behavior and severe sleep disturbance. Little has been reported in the medical literature about anatomical brain anomalies in patients with SMS. Here we describe two patients with SMS caused by the common deletion in 17p11.2 diagnosed using chromosomal microarray (CMA). Both patients had a typical clinical presentation and abnormal brain magnetic resonance imaging (MRI) findings. One patient had subependymal periventricular gray matter heterotopia, and the second had a thin corpus callosum, a thin brain stem and hypoplasia of the cerebellar vermis. This report discusses the possible abnormal MRI images in SMS and reviews the literature on brain malformations in SMS. Finally, although structural brain malformations in SMS patients are not a common feature, we suggest baseline routine brain imaging in patients with SMS in particular, and in patients with chromosomal microdeletion/microduplication syndromes in general. Structural brain malformations in these patients may affect the decision-making process regarding their management.

Follicular Bronchiolitis in a Child With 1p36 Deletion Syndrome

Chromosome 18p deletion syndrome is caused by total or partial deletion of the short arm of chromosome 18 and associated with cognitive impairment, growth retardation and mild facial dysmorphism. However, most studies on the genotype-phenotype correlations in the 18p region are diagnosed postnatally. Prenatal reports involving 18p deletions are limited. Three pregnant women opted for invasive prenatal testing due to noninvasive prenatal testing indicating high risk for chromosome 18 abnormalities. Karyotypic analysis and chromosomal microarray analysis (CMA) were performed simultaneously. The pregnancy outcomes for all cases were followed up. Meanwhile, we also made a literature review on prenatal phenotypes of 18p deletions. G-banding analysis showed that 2 fetuses presented abnormal karyotypes: 45,XN,der(18)t(18;21)(p11; q11),-21 (case 2) and 46,XN,18p- (case 3). The karyotype of case 1 was normal. Meanwhile, CMA detected 4.37 Mb (case 1), 7.26 Mb (case 2) and 14.97 Mb (case 3) deletions in chromosome 18p region. All 3 pregnancies were terminated finally according to genetic counseling based upon abnormal CMA results. Prenatal diagnosis of 18p deletion syndrome is full of challenges due to the phenotypic diversity, incomplete penetrance and lack of prenatal phenotypes. Increased nuchal translucency and holoprosencephaly are common prenatal phenotypes of distal 18p deletion. For fetuses carrying 18p deletions with atypical sonographic phenotypes, noninvasive prenatal testing could be adopted as an effective approach.

Deletions of chromosome 1p36 affect approximately 1 in 5,000 newborns and are the most common terminal deletions in humans. Medical problems commonly caused by terminal deletions of 1p36 include developmental delay, intellectual disability, seizures, vision problems, hearing loss, short stature, distinctive facial features, brain anomalies, orofacial clefting, congenital heart defects, cardiomyopathy, and renal anomalies. Although 1p36 deletion syndrome is considered clinically recognizable, there is significant phenotypic variation among affected individuals. This variation is due, at least in part, to the genetic heterogeneity seen in 1p36 deletions which include terminal and interstitial deletions of varying lengths located throughout the 30 Mb of DNA that comprise chromosome 1p36. Array-based copy number variant analysis can easily identify genomic regions of 1p36 that are deleted in an affected individual. However, predicting the phenotype of an individual based solely on the location and extent of their 1p36 deletion remains a challenge since most of the genes that contribute to 1p36-related phenotypes have yet to be identified. In addition, haploinsufficiency of more than one gene may contribute to some phenotypes. In this article, we review recent successes in the effort to map and identify the genes and genomic regions that contribute to specific 1p36-related phenotypes. In particular, we highlight evidence implicating MMP23B, GABRD, SKI, PRDM16, KCNAB2, RERE, UBE4B, CASZ1, PDPN, SPEN, ECE1, HSPG2, and LUZP1 in various 1p36 deletion phenotypes.

Case Presentation: Patient 1: Female infant diagnosed with Cri du Chat Syndrome (CdCS) (Fig. 1A), hypoplastic left heart syndrome variant (Fig. 1 B), duodenal atresia (Fig. 1 E, F), IUGR. Chromosomal microarray (CMA) showed a 4.3 Mb deletion at 5p15.33 (Fig. 1A) and a 32.2 Mb duplication of 5q32. Dysmorphisms including hypertelorism, low set ears, and micrognathia were noted. Echocardiogram showed a hypoplastic left ventricle, mitral valve dysplasia (Fig. 1B), dysplastic aortic valve (Fig. 1C), interrupted aortic arch (Fig. 1D). Patient 2: Male infant prenatally diagnosed with aortic valve stenosis, aortic arch hypoplasia (Fig. 1H, I), and IUGR. Multiple dysmorphic features including microcephaly, hypertelorism, down slanting palpebral fissures, and abnormal distal extremities. CMA revealed a large deletion at 5p13.33-p13.2 (Fig 1G). He underwent aortic valvuloplasty complicated by development of a posterior left ventricular wall pseudoaneurysm (Fig. 1J). He later underwent arch reconstruction. At 2 months of age, he was diagnosed with obstructive jaundice requiring a biliary drain (Fig.1K, L). He had been gaining weight and height steadily (Fig.1M, N). We identified 5 more patients with 5p deletions and left outflow tract obstructions (LVOTO) from the Cytogenomics of Cardiovascular Malformations Consortium (Table 1). Discussion: CdCS is the most common 5p deletion syndrome and is associated with mild congenital heart defects in 15-30% of individuals. There is no reported association between LVOTO and 5p deletions. These 7 patients did not all share the same deletions and had high mortality. Further studies are needed to better understand possible genetic etiologies.

Chromosome 1p36 deletion accounts for around 1% of cases of intellectual disability. The pattern of clinical features includes developmental delay, hypotonia, seizures, short stature, intellectual disability, vision and hearing deficits, congenital heart disease, and renal abnormalities. The size of deletion can be variable. We report four cases of 1p36 deletion syndrome detected in the past 3 years in a genetic clinic. One patient was detected by next-generation sequencing, another by chromosomal microarray, and the remaining two by multiplex ligation-dependent probe amplification. We discuss the variable presentations in the four children. Early diagnosis enables better prognostication and further reproductive planning.

Chromosome 1p36 deletion is the most common subtelomeric deletion syndrome characterized by variable features including unique facial appearance, intellectual disability, developmental delay, cardiac defects, seizures and hypotonia. Here, we report a patient with developmental delay, dilated cardiomyopathy, seizures, hirsutism and cutis laxa who was diagnosed with 1p36 deletion syndrome by chromosome microarray analysis. This patient is the first reported case of 1p36 deletion syndrome associated with cutis laxa and our results suggest that the 1p36 region contains one or more genes relevant to cutis laxa. This case also indicates the importance of considering chromosome abnormalities (microdeletion/microduplication syndromes) in patients presenting skin disorders combined with unexplained developmental delay, intellectual disability or multiple congenital abnormalities.