Judith Martin

Phenotypic Heterogeneity of Genomic Disorders and Rare Copy-Number Variants

BACKGROUND Some copy-number variants are associated with genomic disorders with extreme phenotypic heterogeneity. The cause of this variation is unknown, which presents challenges in genetic diagnosis, counseling, and management. METHODS We analyzed the genomes of 2312 children known to carry a copy-number variant associated with intellectual disability and congenital abnormalities, using array comparative genomic hybridization. RESULTS Among the affected children, 10.1% carried a second large copy-number variant in addition to the primary genetic lesion. We identified seven genomic disorders, each defined by a specific copy-number variant, in which the affected children were more likely to carry multiple copy-number variants than were controls. We found that syndromic disorders could be distinguished from those with extreme phenotypic heterogeneity on the basis of the total number of copy-number variants and whether the variants are inherited or de novo. Children who carried two large copy-number variants of unknown clinical significance were eight times as likely to have developmental delay as were controls (odds ratio, 8.16; 95% confidence interval, 5.33 to 13.07; P=2.11×10(-38)). Among affected children, inherited copy-number variants tended to co-occur with a second-site large copy-number variant (Spearman correlation coefficient, 0.66; P<0.001). Boys were more likely than girls to have disorders of phenotypic heterogeneity (P<0.001), and mothers were more likely than fathers to transmit second-site copy-number variants to their offspring (P=0.02). CONCLUSIONS Multiple, large copy-number variants, including those of unknown pathogenic significance, compound to result in a severe clinical presentation, and secondary copy-number variants are preferentially transmitted from maternal carriers. (Funded by the Simons Foundation Autism Research Initiative and the National Institutes of Health.).

Allan-Herndon-Dudley Syndrome and the Monocarboxylate Transporter 8 (MCT8) Gene

Allan-Herndon-Dudley syndrome was among the first of the X-linked mental retardation syndromes to be described (in 1944) and among the first to be regionally mapped on the X chromosome (in 1990). Six large families with the syndrome have been identified, and linkage studies have placed the gene locus in Xq13.2. Mutations in the monocarboxylate transporter 8 gene (MCT8) have been found in each of the six families. One essential function of the protein encoded by this gene appears to be the transport of triiodothyronine into neurons. Abnormal transporter function is reflected in elevated free triiodothyronine and lowered free thyroxine levels in the blood. Infancy and childhood in the Allan-Herndon-Dudley syndrome are marked by hypotonia, weakness, reduced muscle mass, and delay of developmental milestones. Facial manifestations are not distinctive, but the face tends to be elongated with bifrontal narrowing, and the ears are often simply formed or cupped. Some patients have myopathic facies. Generalized weakness is manifested by excessive drooling, forward positioning of the head and neck, failure to ambulate independently, or ataxia in those who do ambulate. Speech is dysarthric or absent altogether. Hypotonia gives way in adult life to spasticity. The hands exhibit dystonic and athetoid posturing and fisting. Cognitive development is severely impaired. No major malformations occur, intrauterine growth is not impaired, and head circumference and genital development are usually normal. Behavior tends to be passive, with little evidence of aggressive or disruptive behavior. Although clinical signs of thyroid dysfunction are usually absent in affected males, the disturbances in blood levels of thyroid hormones suggest the possibility of systematic detection through screening of high-risk populations.

CRTAP AND LEPRE1 MUTATIONS IN RECESSIVE OSTEOGENESIS IMPERFECTA

Autosomal dominant osteogenesis imperfecta (OI) is caused by mutations in the genes (COL1A1 or COL1A2) encoding the chains of type I collagen. Recently, dysregulation of hydroxylation of a single proline residue at position 986 of both the triple‐helical domains of type I collagen α1(I) and type II collagen α1(II) chains has been implicated in the pathogenesis of recessive forms of OI. Two proteins, cartilage‐associated protein (CRTAP) and prolyl‐3‐hydroxylase‐1 (P3H1, encoded by the LEPRE1 gene) form a complex that performs the hydroxylation and brings the prolyl cis‐trans isomerase cyclophilin‐B (CYPB) to the unfolded collagen. In our screen of 78 subjects diagnosed with OI type II or III, we identified three probands with mutations in CRTAP and 16 with mutations in LEPRE1. The latter group includes a mutation in patients from the Irish Traveller population, a genetically isolated community with increased incidence of OI. The clinical features resulting from CRTAP or LEPRE1 loss of function mutations were difficult to distinguish at birth. Infants in both groups had multiple fractures, decreased bone modeling (affecting especially the femurs), and extremely low bone mineral density. Interestingly, “popcorn” epiphyses may reflect underlying cartilaginous and bone dysplasia in this form of OI. These results expand the range of CRTAP/LEPRE1 mutations that result in recessive OI and emphasize the importance of distinguishing recurrence of severe OI of recessive inheritance from those that result from parental germline mosaicism for COL1A1 or COL1A2 mutations. Hum Mutat 0, 1–8, 2008.

Haploinsufficiency of SOX5 at 12p12.1 is associated with developmental delays with prominent language delay, behavior problems, and mild dysmorphic features†

SOX5 encodes a transcription factor involved in the regulation of chondrogenesis and the development of the nervous system. Despite its important developmental roles, SOX5 disruption has yet to be associated with human disease. We report one individual with a reciprocal translocation breakpoint within SOX5, eight individuals with intragenic SOX5 deletions (four are apparently de novo and one inherited from an affected parent), and seven individuals with larger 12p12 deletions encompassing SOX5. Common features in these subjects include prominent speech delay, intellectual disability, behavior abnormalities, and dysmorphic features. The phenotypic impact of the deletions may depend on the location of the deletion and, consequently, which of the three major SOX5 protein isoforms are affected. One intragenic deletion, involving only untranslated exons, was present in a more mildly affected subject, was inherited from a healthy parent and grandparent, and is similar to a deletion found in a control cohort. Therefore, some intragenic SOX5 deletions may have minimal phenotypic effect. Based on the location of the deletions in the subjects compared to the controls, the de novo nature of most of these deletions, and the phenotypic similarities among cases, SOX5 appears to be a dosage‐sensitive, developmentally important gene. Hum Mutat 33:728–740, 2012.

Deletions and duplications of developmental pathway genes in 5q31 contribute to abnormal phenotypes.

Although copy number changes of 5q31 have been rarely reported, deletions have been associated with some common characteristics, such as short stature, failure to thrive, developmental delay (DD)/intellectual disability (ID), club feet, dislocated hips, and dysmorphic features. We report on three individuals with deletions and two individuals with duplications at 5q31, ranging from 3.6 Mb to 8.1 Mb and 830 kb to 3.4 Mb in size, respectively. All five copy number changes are apparently de novo and involve several genes that are important in developmental pathways, including PITX1, SMAD5, and WNT8A. The individuals with deletions have characteristic features including DD, short stature, club feet, cleft or high palate, dysmorphic features, and skeletal anomalies. Haploinsufficiency of PITX1, a transcription factor important for limb development, is likely the cause for the club feet, skeletal anomalies, and cleft/high palate, while additional genes, including SMAD5 and WNT8A, may also contribute to additional phenotypic features. Two patients with deletions also presented with corneal anomalies. To identify a causative gene for the corneal anomalies, we sequenced candidate genes in a family with apparent autosomal dominant keratoconus with suggestive linkage to 5q31, but no mutations in candidate genes were found. The duplications are smaller than the deletions, and the patients with duplications have nonspecific features. Although development is likely affected by increased dosage of the genes in the region, the developmental disruption appears less severe than that seen with deletion.

Identification of a novel polymorphism : The duplication of the NPHP1 (Nephronophthisis 1) gene

Hagit Baris, Bassem A. Bejjani, Wen-Hann Tan, David L. Coulter, Judith A. Martin, Andrea L. Storm, Barbara K. Burton, Sulagna C. Saitta, Marzena Gajecka, Blake C. Ballif, Mira B. Irons, Lisa G. Shaffer, and Virginia E. Kimonis* Division of Genetics, Children’s Hospital Boston and Harvard Medical School, Boston, Massachusetts Signature Genomic Laboratories, LLC, Spokane, Washington Health Research and Education Center, Washington State University, Spokane, Washington Department of Neurology, Children’s Hospital Boston and Harvard Medical School, Boston, Massachusetts Inland Northwest Genetics Clinic, Spokane, Washington Department of Medical Genetics and Metabolism, Children’s Hospital Central California, Madera, California Division of Genetics and Department of Pediatrics, Children’s Memorial Hospital and Northwestern University Feinberg School of Medicine, Chicago, Illinois Division of Human Genetics, The Children’s Hospital of Philadelphia and University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania

Deep sequencing with intronic capture enables identification of an APC exon 10 inversion in a patient with polyposis

Purpose:Single-exon inversions have rarely been described in clinical syndromes and are challenging to detect using Sanger sequencing. We report the case of a 40-year-old woman with adenomatous colon polyps too numerous to count and who had a complex inversion spanning the entire exon 10 in APC (the gene encoding for adenomatous polyposis coli), causing exon skipping and resulting in a frameshift and premature protein truncation.Methods:In this study, we employed complete APC gene sequencing using high-coverage next-generation sequencing by ColoSeq, analysis with BreakDancer and SLOPE software, and confirmatory transcript analysis.Results:ColoSeq identified a complex small genomic rearrangement consisting of an inversion that results in translational skipping of exon 10 in the APC gene. This mutation would not have been detected by traditional sequencing or gene-dosage methods.Conclusion:We report a case of adenomatous polyposis resulting from a complex single-exon inversion. Our report highlights the benefits of large-scale sequencing methods that capture intronic sequences with high enough depth of coverage—as well as the use of informatics tools—to enable detection of small pathogenic structural rearrangements.Genet Med 16 10, 783–786.

Hepatoblastoma in a male with MECP2 duplication syndrome.

Conflict of interest: none. Correspondence to: Angela Trobaugh-Lotrario, M.D., Department of Pediatric Hematology/ Oncology, Sacred Heart Children’s Hospital, 101West 8th Avenue, Spokane WA 99204. E-mail: angela.trobaugh@providence.org Article first published online in Wiley Online Library (wileyonlinelibrary.com): 24 November 2015 DOI 10.1002/ajmg.a.37474 How to Cite this Article: Trobaugh-Lotrario A, Martin J, L opez-Terrada D. 2016. Hepatoblastoma in a male with MECP2 duplication syndrome.

Familial 25.3 Mb inverted duplication of bands q32.1 to q35.1 on chromosome 4 with psychomotor impairments

Partial 4q trisomy has been described in more than 80 patients. In most patients, the 4q trisomic segment was derived from a parent carrying a reciprocal balanced translocation or an inversion on chromosome 4 and was accompanied by a concurrent deletion of another chromosomeor a short armof chromosome4, respectively. Clinical heterogeneity of partial 4q trisomy has been reported, possibly due to the variability of the 4q duplicated segment and its accompanied anomalies. Pure duplications of 4q without a concurrent deletion are infrequent and have been described in fewer than 25 patients [Celle et al., 2000; Rinaldi et al., 2003; Lin et al., 2004; Otsuka et al., 2005; Egritas et al., 2010]. Here we present a three-generation family with pure 4q32.1-q35.1 duplication, never described before (Fig. 1). This 25.3Mb 4q duplication was detected by conventional chromosome study and was further characterized by SNP microarray analyses and FISH studies. The patient was a 4-month-old male with failure to progress, who was born to a 33-year-old mother at 41 weeks gestational age by cesarean. At birth, he was in the neonatal intensive care unit for 6 days because of respiratory distress. Subsequently, at 2months of age, he had an episode of apnea andwas hospitalized. At this time, he was diagnosed with a fenestrated atrial shunt, mild supravalvar pulmonic stenosis, and gastroesophageal reflux disease. At the age of 4 months (Fig. 1, III-2), his height was at the 50th centile, his weight was at the 90th centile, and his OFC was at the 75th centile. He had developmental delay, large anterior fontanelle, broad cheeks, bilateral epicanthal folds, and long philtrum. He had bilateral single transverse palmar creases, deep creases in the soles of his feet, hypoplastic nails, and right-side cryptorchidism. Otherwise, his general physical examination was unremarkable. His 34-year-oldmother, his 56-year-oldmaternal grandmother, his 35-year-old maternal aunt (Fig. 1, II-1), and his 14-year-old maternal cousin (Fig. 1, III-1) had psychomotor impairments and needed special education. His 59-year-old maternal grandfather (Fig. 1, I-2) is phenotypically normal and his father is not available. The patient’s blood karyotype is 46,XY,dup(4)(q35q32) resulting in an interstitial duplication of the 4q32-q35 segment (Fig. 2a), which was further delineated by chromosomemicroarray analyses. Affymetrix Genome-wide 6.0 SNP-microarray genotyping (using Chromosome Analysis Suite software for the analysis) showed a 25.3Mb duplication of a chromosome 4 [arr 4q32.1q35.1 (158,425,313–183,681,864)X3] using the assembly hg19/GRCh 37 of the human genome (Fig. 2b). FISH was performed using home-brewed BAC probes including RP11-719M18 at 4q32 and RP11-295A7 at 4q35. FISH analysis confirmed this 4q duplication since these probes showed three copies in each of 200 interphase