Genome-wide linkage and copy number variation analysis reveals 710 kb duplication on chromosome 1p31.3 responsible for autosomal dominant omphalocele.

BACKGROUND: Omphalocele is a congenital birth defect characterised by the presence of internal organs located outside of the ventral abdominal wall. The purpose of this study was to identify the underlying genetic mechanisms of a large autosomal dominant Caucasian family with omphalocele. METHODS AND FINDINGS: A genetic linkage study was conducted in a large family with an autosomal dominant transmission of an omphalocele using a genome-wide single nucleotide polymorphism (SNP) array. The analysis revealed significant evidence of linkage (non-parametric NPL = 6.93, p=0.0001; parametric logarithm of odds (LOD) = 2.70 under a fully penetrant dominant model) at chromosome band 1p31.3. Haplotype analysis narrowed the locus to a 2.74 Mb region between markers rs2886770 (63014807 bp) and rs1343981 (65757349 bp). Molecular characterisation of this interval using array comparative genomic hybridisation followed by quantitative microsphere hybridisation analysis revealed a 710 kb duplication located at 63.5-64.2 Mb. All affected individuals who had an omphalocele and shared the haplotype were positive for this duplicated region, while the duplication was absent from all normal individuals of this family. Multipoint linkage analysis using the duplication as a marker yielded a maximum LOD score of 3.2 at 1p31.3 under a dominant model. The 710 kb duplication at 1p31.3 band contains seven known genes including FOXD3, ALG6, ITGB3BP, KIAA1799, DLEU2L, PGM1, and the proximal portion of ROR1. Importantly, this duplication is absent from the database of genomic variants. CONCLUSIONS: The present study suggests that development of an omphalocele in this family is controlled by overexpression of one or more genes in the duplicated region. To the authors' knowledge, this is the first reported association of an inherited omphalocele condition with a chromosomal rearrangement.

Complete Genome Sequence of Bradyrhizobium japonicum Podophage Paso.

Bradyrhizobium japonicum is a nitrogen-fixing, Gram-negative bacterium that forms a symbiotic relationship with leguminous plants. This announcement describes the isolation and genome annotation of B. japonicum T7-like podophage Paso. Genomic analysis reveals genes that are associated with both the T5 and T7 modes of genomic DNA entry into the host.

Complete Genome Sequence of Rhizobium phaseoli Podophage Palo.

Here, we present the genome of Palo, a T7-like podophage of Rhizobium phaseoli The genome is 46.3 kb and contains 58 predicted protein-coding genes, including a novel signal-anchor-release (SAR) endolysin, a homolog of the T5 A1 protein required for DNA transfer, and a dual-start holin/antiholin pair.

Complete Genome Sequence of Rhizobium japonicum Podophage Pasto.

Rhizobium japonicum is a Gram-negative bacterium of interest for research into nitrogen fixation in legumes. This article describes the isolation, sequencing, and annotation of R. japonicum podophage Pasto. While it shows no significant similarity to identified phages, genomic analysis indicates that Pasto may be temperate and is a novel T7-like podophage.

Complete Genome Sequence of Salmonella enterica Siphophage Shemara.

Here, we present the annotated genome of Shemara, a siphophage of Salmonella enterica The Shemara genome is 44 kb with 83 predicted protein-coding genes. At the nucleotide and amino acid levels, Shemara is most similar to phages in the Guernseyvirinae subfamily.

Complete Genome Sequence of Serratia marcescens Siphophage Slocum.

Serratia marcescens is a ubiquitous Gram-negative opportunistic pathogen. This announcement describes the isolation and genome annotation of S. marcescens T5-like siphophage Slocum. Terminal repeats, 170 protein-coding genes, and 23 tRNAs were predicted in the 112,436-bp Slocum genome.

Complete Genome Sequence of Stenotrophomonas Phage Mendera.

Stenotrophomonas maltophilia is an emerging opportunistic human pathogen. In this report, we describe the isolation and genomic annotation of the S. maltophilia-infecting bacteriophage Mendera. A myophage of 159,961 base pairs, Mendera is T4-like and related most closely to Stenotrophomonas phage IME-SM1.

Complete Genome Sequence of Stenotrophomonas maltophilia Myophage Moby.

Stenotrophomonas maltophilia is a prevalent nosocomial pathogen with multidrug resistance. Here, we describe the complete genome of S. maltophilia myophage Moby, which shares characteristics with Enterobacteria phage T4 and is closely related to Stenotrophomonas phage IME-SM1. Moby has a 159,365-bp genome with 271 predicted protein-coding genes and 24 predicted tRNAs.

Complete Genome Sequence of Escherichia coli Siphophage Schulenberg.

Escherichia coli bacteria and their infecting bacteriophage exist within the gut. Here, we present the complete genome of Schulenberg, an E. coli siphophage similar to phages of the subfamily Guernseyvirinae Schulenberg encodes 85 proteins, 33 of which have predicted functions.

Complete Genome Sequence of Serratia marcescens Myophage Moabite.

Serratia marcescens is a Gram-negative nosocomial pathogen causing various hospital-acquired infections. Here, we describe the complete genome sequence of S. marcescens myophage Moabite. The genome of Moabite is 273,933 bp long, with 337 predicted coding sequences and two tRNA genes, and it shares its highest amino acid identity with Serratia phage 2050HW.

Complete Genome Sequence of Klebsiella pneumoniae Myophage Menlow.

Klebsiella pneumoniae is an opportunistic pathogen that has become an increasing problem in nosocomial infections. Studying phages that infect K. pneumoniae may lead to improvements in phage therapeutics for treating these infections. Here, the full genome sequence of Menlow, a Vi01-like phage, is introduced and described.

Complete Genome Sequence of Escherichia coli Myophage Minorna.

The Gram-negative bacterium Escherichia coli causes many diseases, and antibiotic resistance has become a problem for their treatment. Bacteriophages may present a viable treatment alternative. Here, the complete genome sequence of E. coli-infecting myophage Minorna is presented. Proteins needed for replication, morphogenesis, and lysis were identified in the Minorna coding sequence.

Coding-Complete Genome Sequence of Staphylococcus aureus Podophage Portland.

Staphylococcus aureus bacteria, especially the multidrug resistance strains, are responsible for a wide range of clinical infections. Here, we announce the genome sequence of S. aureus podophage Portland, which is closely related to a group of phi29-like S. aureus podophages, including phages phi44AHJD and phiP68. The exact genome sequence ends of phage Portland were not determined and may be obscured by terminal proteins.

Complete Genome Sequence of Salmonella enterica Myophage Matapan.

Here, we describe the Salmonella enterica serovar Heidelberg phage Matapan. A myophage with a 157,408-kb genome, Matapan is most closely related to Vi01-like phages.

Complete Genome Sequence of Shelby, a Siphophage Infecting Carbapenemase-Producing Klebsiella pneumoniae.

Carbapenem-resistant Klebsiella pneumoniae, a bacterium of the family Enterobacteriaceae, is a high-priority antibiotic-resistant pathogen that causes nosocomial infections. Here, we describe the isolation and annotation of the K. pneumoniae siphophage Shelby, a T1-like siphophage encoding 78 proteins, of which 34 have a predicted function.

Complete Genome Sequence of Serratia marcescens Myophage MyoSmar.

Serratia marcescens is an opportunistic pathogen that causes respiratory, urinary, and digestive tract infections in humans. Here, we describe the annotation of Serratia marcescens myophage MyoSmar. The 68,745-bp genome encodes 105 predicted proteins and is most similar to the genomes of Pseudomonas PB1-like viruses.

Complete Genome Sequence of Stenotrophomonas maltophilia Podophage Ponderosa.

Stenotrophomonas maltophilia is a Gram-negative bacterium that is emerging as a multidrug-resistant global opportunistic pathogen. Here, we describe the genome of the T7-like S. maltophilia podophage Ponderosa, with 54 predicted protein-coding genes and a 493-bp terminal repeat.

Complete Genome Sequence of Salmonella enterica Siphophage Shelanagig.

Salmonella enterica is a Gram-negative human pathogen widely known to cause food poisoning. Here, the genome of S. enterica phage Shelanagig is described. Its 42,541-bp genome codes for 68 proteins, for which 33 were assigned a predicted function. Shelanagig shares high similarity at the protein level with other Salmonella phages.

Complete Genome Sequence of Klebsiella pneumoniae Siphophage Skenny.

Klebsiella pneumoniae is a Gram-negative opportunistic pathogen and a leading cause of antibiotic-resistant nosocomial infections. The genome sequence of siphophage Skenny, which infects K. pneumoniae, is described here. Skenny encodes 78 genes and is closely related to Klebsiella phages KPN N141 and MezzoGao, which are T1-like phages.

Complete Genome Sequence of Klebsiella pneumoniae Phage Sweeny.

Klebsiella pneumoniae is a multidrug-resistant bacterium causing many severe hospital-acquired infections. Here, we describe siphophage Sweeny that infects K. pneumoniae Of its 78 predicted protein-encoding genes, a functional assignment was given to 36 of them. Sweeny is most closely related to T1-like phages at the protein level.