Carlos A. Bacino

Alu-mediated diverse and complex pathogenic copy-number variants within human chromosome 17 at p13.3

Alu repetitive elements are known to be major contributors to genome instability by generating Alu-mediated copy-number variants (CNVs). Most of the reported Alu-mediated CNVs are simple deletions and duplications, and the mechanism underlying Alu-Alu-mediated rearrangement has been attributed to non-allelic homologous recombination (NAHR). Chromosome 17 at the p13.3 genomic region lacks extensive low-copy repeat architecture; however, it is highly enriched for Alu repetitive elements, with a fraction of 30% of total sequence annotated in the human reference genome, compared with the 10% genome-wide and 18% on chromosome 17. We conducted mechanistic studies of the 17p13.3 CNVs by performing high-density oligonucleotide array comparative genomic hybridization, specifically interrogating the 17p13.3 region with ∼150 bp per probe density; CNV breakpoint junctions were mapped to nucleotide resolution by polymerase chain reaction and Sanger sequencing. Studied rearrangements include 5 interstitial deletions, 14 tandem duplications, 7 terminal deletions and 13 complex genomic rearrangements (CGRs). Within the 17p13.3 region, Alu-Alu-mediated rearrangements were identified in 80% of the interstitial deletions, 46% of the tandem duplications and 50% of the CGRs, indicating that this mechanism was a major contributor for formation of breakpoint junctions. Our studies suggest that Alu repetitive elements facilitate formation of non-recurrent CNVs, CGRs and other structural aberrations of chromosome 17 at p13.3. The common observation of Alu-mediated rearrangement in CGRs and breakpoint junction sequences analysis further demonstrates that this type of mechanism is unlikely attributed to NAHR, but rather may be due to a recombination-coupled DNA replicative repair process.

De Novo Disruption of the Proteasome Regulatory Subunit PSMD12 Causes a Syndromic Neurodevelopmental Disorder

Degradation of proteins by the ubiquitin-proteasome system (UPS) is an essential biological process in the development of eukaryotic organisms. Dysregulation of this mechanism leads to numerous human neurodegenerative or neurodevelopmental disorders. Through a multi-center collaboration, we identified six de novo genomic deletions and four de novo point mutations involving PSMD12, encoding the non-ATPase subunit PSMD12 (aka RPN5) of the 19S regulator of 26S proteasome complex, in unrelated individuals with intellectual disability, congenital malformations, ophthalmologic anomalies, feeding difficulties, deafness, and subtle dysmorphic facial features. We observed reduced PSMD12 levels and an accumulation of ubiquitinated proteins without any impairment of proteasome catalytic activity. Our PSMD12 loss-of-function zebrafish CRISPR/Cas9 model exhibited microcephaly, decreased convolution of the renal tubules, and abnormal craniofacial morphology. Our data support the biological importance of PSMD12 as a scaffolding subunit in proteasome function during development and neurogenesis in particular; they enable the definition of a neurodevelopmental disorder due to PSMD12 variants, expanding the phenotypic spectrum of UPS-dependent disorders.

A homozygous mutation in PEX16 identified by whole-exome sequencing ending a diagnostic odyssey

We present a patient with a unique neurological phenotype with a progressive neurodegenerative. An 18-year diagnostic odyssey for the patient ended when exome sequencing identified a homozygous PEX16 mutation suggesting an atypical peroxisomal biogenesis disorder (PBD). Interestingly, the patients peroxisomal biochemical abnormalities were subtle, such that plasma very-long-chain fatty acids initially failed to provide a diagnosis. This case suggests that next-generation sequencing may be diagnostic in some atypical peroxisomal biogenesis disorders.

Dataset for a case report of a homozygous PEX16 F332del mutation

This dataset provides a clinical description along with extensive biochemical and molecular characterization of a patient with a homozygous mutation in PEX16 with an atypical phenotype. This patient described in Molecular Genetics and Metabolism Reports was ultimately diagnosed with an atypical peroxisomal disorder on exome sequencing. A clinical timeline and diagnostic summary, results of an extensive plasma and fibroblast analysis of this patient׳s peroxisomal profile is provided. In addition, a table of additional variants from the exome analysis is provided.

Novel deletion of 6p21.31p21.1 associated with laryngeal cleft, developmental delay, dysmorphic features and vascular anomaly

Interstitial deletions involving chromosome region 6p21.31p21.2 have not been previously reported in the literature. Here, we present a 2 year old girl with global developmental delay, severe speech delay, dysmorphic features, laryngeal cleft, anterior descending aorta that occluded the left main bronchus and a novel de novo deletion of chromosome 6: arr[hg19] 6p21.31p21.2 (35462950-36725083)x1. The deletion, which was diagnosed by array comparative genomic hybridization and further confirmed with fluorescence in situ hybridization, was approximately 1.26 Mb and contained 28 RefSeq genes. The deleted region includes 24 protein coding genes and 4 non-coding genes. This represents a novel microdeletion that has not been previously reported in the literature.

Re: Familial cryptic translocation (2;17) ascertained through recurrent spontaneous abortions: Bruyere H, Rajcan-Separovic E, Doyle J, Pantzar T, Langlois S

We read with interest the article recently published in your Journal with regards to a familial cryptic translocation involving the distal end of chromosome arms 2q and 17q. The described family was initially ascertained through a woman who presented with a history of three recurrent miscarriages, and two pregnancies that resulted in neonatal deaths. Shewas later found to have a cryptic balanced translocation involving the distal ends of chromosome arms 2q and 17q. Cytogenetic studies performed on one of two twins from one of her pregnancies that presented with multiple congenital anomalies showed that he inherited the unbalanced derivative 2 from the mother giving this fetus monosomy for distal 2q and trisomy for distal 17q [Bruyere et al., 2003]. The authors unfortunately failed to completely review the literature with regards to this translocation, and therefore they missed an article published by the Journal addressing the same abnormality [Bacino et al., 2000]. In that article, we reporteda family of Iraniandescent diagnosedwithapparently the same chromosome rearrangement. The proposita, who initially presented for evaluation, had the unbalanced derivative chromosome 2 as reported by Bruyere et al. [2003] with monosomy 2q and trisomy 17q which in our case was inherited from the father who was the carrier of a balanced 2q;17q rearrangement. She had severe mental retardation and multiple anomalies. This family also presents with a significant history of multiple miscarriages (eight miscarriages in two generations), and six children with multiple congenital anomalies, some resulting in neonatal deaths. We agree with Bruyere et al. [2003] regarding the need to determine the incidence of subtelomeric rearrangements in families with multiple miscarriages. The literature thus far has not supported the need to study couples with recurrent miscarriages with subtelomeric FISH testing. This assay is mostly reserved for childrenwith unexplainedmental retardation, and in particular for cases in which there is a family history of recurrent anomalies andmental retardation [Knight et al., 1999; Knight and Flint, 2000]. Although this subject has been revisited numerous times, no consensus has been reached as to whether couples that present for evaluation secondary to multiple miscarriages should be screened for the presence of cryptic chromosome rearrangements. Some studies have shown no link between subtelomeric cryptic rearrangements andmultiple miscarriages [Jalal et al., 2001; Benzacken et al., 2002; Fan and Zhang, 2002] while others have shown subtelomeric rearrangements [Brackley et al., 1999; Yakut et al., 2002; Cockwell et al., 2003]. In fact, one of those studies found 6 such subtelomeric rearrangements among 50 couples that presented with 3 or more spontaneous pregnancy losses [Cockwell et al., 2003]. The report of this second family with a 2q;17q cryptic rearrangement brings up the subject again and poses the question: is it prudent to do subtelomeric FISH studies in couples with recurrent miscarriages in addition to G-banded chromosome analysis? Is the 2q;17q cryptic translocation a more common occurrence than previously anticipated? A recent article in the Journal [McKenzie et al., 2003] examined preimplantation genetic diagnosis (PGD) in the family previously reported by our group. In this family, a total of 26 embryos were studied by PGD following three cycles of in vitro fertilization (IVF) however, only18 of those embryos were informative. Six out of the 18 embryos were chromosomally normal/balanced (33%). Among the 12 abnormal products found on the biopsies, 7 of them (39%) were the result of an adjacent-1 segregation with 4 embryos showingmonosomy 2q, trisomy 17q and 3 embryos showing trisomy 2q and monsomy 17q. It is also of interest that five of the abnormal embryos resulted from a 3:1 segregation (28%), an outcome not theoretically expected given the segments involved in the translocation. Overall we would have expected a higher number of alternate segregation products and no 3:1 products with tertiary trisomies. Although it is difficult to extrapolate the in vitro information to what occurs in vivo, it is tempting to hypothesize that subtelomeric translocations behave quite differently from other reciprocal translocations involving larger segments. It is also tempting to speculate that pairing at the subtelomeric regions is so important for proper segregation that subtelomeric rearrangements result inhigher rates of and unpredictable modes of malsegregation. This notion is supported by studies showing polymorphic differences in subtelomeric regions like in 16pter, where recombination suppression has been seen between divergent alleles that show difference in (CA)n lengths [Wilkie and Higgs, 1992]. Based on the cases reviewed here [Bacino et al., 2000; Yakut et al., 2002; Bruyere et al., 2003, Cockwell et al., 2003], continued systematic searches for cryptic subtelomeric rearrangements in couples with multiple miscarriages seems well worth investigating.