Hereditary cancer syndrome-associated pathogenic variants are common in patients with hematologic malignancies subsequent to primary solid cancer.

As the number of long-term survivors of solid cancers keeps increasing, risk assessment of secondary hematologic malignancies is important for the prognosis of the patient. Germline genetic predisposition to secondary hematologic malignancy has been studied widely in myeloid neoplasms and rarely in lymphoid neoplasms. This study aimed to profile the mutational spectrums of patients with subsequent lymphoid tissue neoplasm to shed some light on the understudied area.

Quantitative and Qualitative QC of Next-Generation Sequencing for Detecting Somatic Variants: An Example of Detecting Clonal Hematopoiesis of Indeterminate Potential.

Background: Because next-generation sequencing (NGS) for detecting somatic mutations has been adopted in clinical fields, both qualitative and quantitative QC of the somatic variants through whole coding regions detected by NGS is crucial. However, specific applications or guidelines, especially for quantitative QC, are currently insufficient. Our goal was to devise a practical approach for both quantitative and qualitative QC using an example of detecting clonal hematopoiesis of indeterminate potential (CHIP).

DeviCNV: detection and visualization of exon-level copy number variants in targeted next-generation sequencing data.

Background: Targeted next-generation sequencing (NGS) is increasingly being adopted in clinical laboratories for genomic diagnostic tests.

Results: We developed a new computational method, DeviCNV, intended for the detection of exon-level copy number variants (CNVs) in targeted NGS data. DeviCNV builds linear regression models with bootstrapping for every probe to capture the relationship between read depth of an individual probe and the median of read depth values of all probes in the sample.

A New Integrated Newborn Screening Workflow Can Provide a Shortcut to Differential Diagnosis and Confirmation of Inherited Metabolic Diseases.

Purpose: We developed a new workflow design which included results from both biochemical and targeted gene sequencing analysis interpreted comprehensively. We then conducted a pilot study to evaluate the benefit of this new approach in newborn screening (NBS) and demonstrated the efficiency of this workflow in detecting causative genetic variants.

Materials And Methods: Ten patients in Group 1 were diagnosed clinically using biochemical assays only, and 10 newborns in Group 2 were diagnosed with suspected inherited metabolic disease (IMD) in NBS.

Mutations in DDX58, which encodes RIG-I, cause atypical Singleton-Merten syndrome.

Singleton-Merten syndrome (SMS) is an autosomal-dominant multi-system disorder characterized by dental dysplasia, aortic calcification, skeletal abnormalities, glaucoma, psoriasis, and other conditions. Despite an apparent autosomal-dominant pattern of inheritance, the genetic background of SMS and information about its phenotypic heterogeneity remain unknown. Recently, we found a family affected by glaucoma, aortic calcification, and skeletal abnormalities.

Bacterial genome mapper: A comparative bacterial genome mapping tool.

Unlabelled: Recently, next generation sequencing (NGS) technologies have led to a revolutionary increase in sequencing speed and costefficacy. Consequently, a vast number of contigs from many recently sequenced bacterial genomes remain to be accurately mapped and annotated, requiring the development of more convenient bioinformatics programs. In this paper, we present a newly developed web-based bioinformatics program, Bacterial Genome Mapper, which is suitable for mapping and annotating contigs that have been assembled from bacterial genome sequence raw data.

CACG: a database for comparative analysis of conjoined genes.

A conjoined gene is defined as one formed at the time of transcription by combining at least part of one exon from each of two or more distinct genes that lie on the same chromosome, in the same or opposite orientation, which translate independently into different proteins. We comparatively studied the extent of conjoined genes in thirteen genomes by analyzing the public databases of expressed sequence tags and mRNA sequences using a set of computational tools designed to identify conjoined genes on the same DNA strand or opposite DNA strands of the same genomic locus. The CACG database, available at http://cgc.

Genome sequence of the anaerobic bacterium Clostridium arbusti SL206(T).

A new Clostridium species has been isolated from pear orchard soil in Daejeon, Republic of Korea. The isolate, Clostridium arbusti SL206(T) (KCTC 5449(T)), showed a nitrogenase activity as well as an organic acid production. Here we first report the draft genome sequence of a novel species in the genus Clostridium within the largest Gram-positive group.

Genome sequence of Myroides injenensis M09-0166(T), isolated from clinical specimens.

A new Myroides species has been isolated from the urine of a patient with fever in spite of multiple antibiotic treatments who had undergone a radical hysterectomy for cervical cancer and percutaneous nephrostomies for hydronephrosis in the past. The isolate, Myroides injenensis M09-0166(T) (KCTC 23367(T)), showed a high level of resistance to multiple antibiotic agents. Here we provide the first report of the draft genome sequence of a novel species in the genus Myroides within the nonfermenting Gram-negative group.

Genome sequence of Peptoniphilus rhinitidis 1-13T, an anaerobic coccus strain isolated from clinical specimens.

A new Peptoniphilus species has been isolated from samples from a patient who was scheduled for endoscopic sinus surgery for chronic rhinosinusitis. The isolate, Peptoniphilus rhinitidis 1-13(T) (KCTC 5985(T)), can use peptone as a sole carbon source and produce butyrate as a metabolic end product. This is the first report of the draft genome sequence of a novel species in the genus Peptoniphilus within the group of Gram-positive anaerobic cocci.

Genome analysis of the domestic dog (Korean Jindo) by massively parallel sequencing.

Although pioneering sequencing projects have shed light on the boxer and poodle genomes, a number of challenges need to be met before the sequencing and annotation of the dog genome can be considered complete. Here, we present the DNA sequence of the Jindo dog genome, sequenced to 45-fold average coverage using Illumina massively parallel sequencing technology. A comparison of the sequence to the reference boxer genome led to the identification of 4 675 437 single nucleotide polymorphisms (SNPs, including 3 346 058 novel SNPs), 71 642 indels and 8131 structural variations.

Genome sequence of Lactobacillus fructivorans KCTC 3543.

Lactobacillus fructivorans is important in the generation of particular flavors and in other ripening processes associated with fermented food. Here, we present the draft genome sequence of the type strain Lactobacillus fructivorans KCTC 3543 (1,373,326 bp, with a G+C content of 38.9%), which consists of 5 scaffolds.

SpiroESTdb: a transcriptome database and online tool for sparganum expressed sequences tags.

Background: Sparganum (plerocercoid of Spirometra erinacei) is a parasite that possesses the remarkable ability to survive by successfully modifying its physiology and morphology to suit various hosts and can be found in various tissues, even the nervous system. However, surprisingly little is known about the molecular function of genes that are expressed during the course of the parasite life cycle. To begin to decipher the molecular processes underlying gene function, we constructed a database of expressed sequence tags (ESTs) generated from sparganum.

Novel mechanism of conjoined gene formation in the human genome.

Recently, conjoined genes (CGs) have emerged as important genetic factors necessary for understanding the human genome. However, their formation mechanism and precise structures have remained mysterious. Based on a detailed structural analysis of 57 human CG transcript variants (CGTVs, discovered in this study) and all (833) known CGs in the human genome, we discovered that the poly(A) signal site from the upstream parent gene region is completely removed via the skipping or truncation of the final exon; consequently, CG transcription is terminated at the poly(A) signal site of the downstream parent gene.

Genome sequence of Leuconostoc carnosum KCTC 3525.

We announce the draft genome sequence of the type strain Leuconostoc carnosum KCTC 3525 (3,234,408 bp with a G+C content of 40.9%), one of the most prevalent lactic acid bacteria present during the manufacturing process of vacuum-packaged meats, which consists of 2,407 large contigs (>500 bp in size). The genome sequence was obtained by a whole-genome shotgun strategy using Roche 454 GS (FLX Titanium) pyrosequencing, and all of the reads were assembled using Newbler Assembler 2.

Genome sequence of Lactobacillus versmoldensis KCTC 3814.

Lactobacillus versmoldensis KCTC 3814 was isolated from raw fermented poultry salami. The species was present in high numbers and frequently dominated the lactic acid bacteria (LAB) populations of the products. Here, we announce the draft genome sequence of Lactobacillus versmoldensis KCTC 3814, isolated from poultry salami, and describe major findings from its annotation.

Draft genome sequence of Lactobacillus malefermentans KCTC 3548.

We announce the draft genome sequence of the type strain Lactobacillus malefermentans KCTC 3548 (2,003,922 bp, with a G+C content of 41.1%), which is one of the most prevalent lactic acid bacteria present during the manufacturing process of beer; the genome consists of 172 large contigs (>100 bp in size). All of the contigs were assembled by using Newbler Assembler 2.

Genome sequence of Lactobacillus suebicus KCTC 3549.

Lactobacillus suebicus is important in the generation of particular flavors and in other ripening processes associated with apple mash. Here, we present the draft genome sequence of the type strain Lactobacillus suebicus KCTC 3549 (2,656,936 bp, with a G+C content of 39.0%), which consists of 143 large contigs (>100 bp).

Draft genome sequence of Lactobacillus zeae KCTC 3804.

We announce the draft genome sequence of the type strain Lactobacillus zeae KCTC 3804 (3,110,326 bp, with a G+C content of 47.8%), which is one of the most prevalent lactic acid bacteria present during the processing of raw cow's milk. The genome consists of 113 large contigs (>100 bp).

Draft genome sequence of Lactobacillus mali KCTC 3596.

We announce the draft genome sequence of the type strain Lactobacillus mali KCTC 3596 (2,652,969 bp, with a G+C content of 36.0%), which is one of the most prevalent lactic acid bacteria present during the manufacturing process of apple juice. The genome consists of 122 large contigs (>100 bp).

Genome sequence of Lactobacillus cypricasei KCTC 13900.

Lactobacillus cypricasei KCTC 13900 is important in the generation of particular flavors and in other ripening processes associated with specific cheeses. Here, we announce the draft genome sequence of Lactobacillus cypricasei KCTC 13900, isolated from cheeses, and describe major findings from its annotation.

Genome sequence of Leuconostoc pseudomesenteroides KCTC 3652.

We announce the genome sequence of one of the most prevalent lactic acid bacteria present during the manufacturing process of cane juice, the type strain Leuconostoc pseudomesenteroides KCTC 3652 (3,244,985 bp, with a G+C content of 38.3%), which consists of 1,160 large contigs (>100 bp in size). All of the contigs were assembled by the Newbler Assembler 2.

Major chimpanzee-specific structural changes in sperm development-associated genes.

A comprehensive analysis of transcriptional structures of chimpanzee sperm development-associated genes is of significant interest for deeply understanding sperm development and male reproductive process. In this study, we sequenced 7,680 clones from a chimpanzee testis full-length cDNA library and obtained 1,933 nonredundant high-quality full-length cDNA sequences. Comparative analysis between human and chimpanzee showed that 78 sperm development-associated genes, most of which were yet uncharacterized, had undergone severe structural changes (mutations at the start/stop codons, INDELs, alternative splicing variations and fusion forms) on genomic and transcript levels throughout chimpanzee evolution.

Genome sequence of Lactobacillus farciminis KCTC 3681.

Lactobacillus farciminis is one of the most prevalent lactic acid bacterial species present during the manufacturing process of kimchi, the best-known traditional Korean dish. Here, we present the draft genome sequence of the type strain Lactobacillus farciminis KCTC 3681 (2,498,309 bp, with a G+C content of 36.4%), which consists of 5 scaffolds.