Acute Myeloid Leukemia and Next-Generation Sequencing Panels for Diagnosis: A Comprehensive Review.

Acute myeloid leukemia (AML) is a genetically heterogeneous clonal disorder characterized by the accumulation of acquired somatic genetic alterations in hematopoietic progenitor cells, which alter the normal mechanisms of self-renewal, proliferation, and differentiation. Due to significant technological advancements in sequencing technologies in the last 2 decades, classification and prognostic scoring of AML has been refined, and multiple guidelines are now available for the same. The authors have tried to summarize, latest guidelines for AML diagnosis, important markers associated, epigenetics markers, various AML fusions and their importance, etc. Review of literature suggests lack of study or comprehensive information about current NGS panels for AML diagnosis, genes and fusions covered, their technical know-how, etc. To solve this issue, the authors have tried to present detailed review about currently in use next-generation sequencing myeloid panels and their offerings.

Elicitation of Diosgenin Production in Trigonella foenum-graecum (Fenugreek) Seedlings by Methyl Jasmonate.

The effects of methyl jasmonate (MeJA), an elicitor of plant defense mechanisms, on the biosynthesis of diosgenin, a steroidal saponin, were investigated in six fenugreek (Trigonella foenum-graecum) varieties (Gujarat Methi-2, Kasuri-1, Kasuri-2, Pusa Early Branching, Rajasthan Methi and Maharashtra Methi-5). Treatment with 0.01% MeJA increased diosgenin levels, in 12 days old seedlings, from 0.5%-0.9% to 1.1%-1.8%. In addition, MeJA upregulated the expression of two pivotal genes of the mevalonate pathway, the metabolic route leading to diosgenin: 3-hydroxy-3-methylglutaryl-CoA reductase (HMG) and sterol-3-ß-glucosyl transferase (STRL). In particular, MeJA increased the expression of HMG and STRL genes by 3.2- and 22.2-fold, respectively, in the Gujarat Methi-2 variety, and by 25.4- and 28.4-fold, respectively, in the Kasuri-2 variety. Therefore, MeJA may be considered a promising elicitor for diosgenin production by fenugreek plants.

Author Correction: Whole exome sequencing reveals rare variants linked to congenital pouch colon.

A correction to this article has been published and is linked from the HTML and PDF versions of this paper. The error has been fixed in the paper.

Whole exome sequencing reveals rare variants linked to congenital pouch colon.

We demonstrate the application of whole exome sequencing to discover the rare variants for congenital pouch colon, acronymed CPC. For 18 affected individuals in a total of 64 samples, we sequenced coding regions to a mean coverage of 100×. A sufficient depth of ca. 94% of targeted exomes was achieved. Filtering against the public SNP/variant repositories, we identified a host of candidate genes, EPB41L4A and CTC1 associated with colon, neural/brain muscles and Dyskeratosis Congenita maladies. Furthermore, the stop gain mutations in the form of JAG1,OR5AR1,SLC22A24,PEX16,TSPAN32,TAF1B,MAP2K3 and SLC25A19 appears to be localized to Chromosomes 2, 11, 17 and 20 in addition to the three stop lost mutants across three genes, viz. OAS2, GBA3 and PKD1L2 affecting the colon tissue. While our results have paved way for transcendence of monogenic traits in identifying the genes underlying rare genetic disorders, it will provide helpful clues for further investigating genetic factors associated with anorectal anomalies, particularly CPC.

Validation of a method for diosgenin extraction from fenugreek (Trigonella foenum-graecum L.).

BACKGROUND: Diosgenin is a very important plant secondary metabolite and raw material for the drug indus- try. Plant sources rich in diosgenin include yam (Dioscorea spp.) and fenugreek (Trigonella foenum-graecum L.). A method for diosgenin extraction from yam extracts has previously been validated, but its extraction from fenugreek plants still requires validation. In addition, all available methods require time-consuming additional purification steps. The present study was aimed at developing a low cost, less time-consuming single-step method for diosgenin extraction from fenugreek. METHODS: This study represents a method developed for diosgenin extraction from fenugreek plants without any additional/supportive purification methods such as chromatography or thin-layer chroma- tography. Diosgenin yield estimation and purity analysis by HPLC method, along with accuracy and preci- sion analysis, is presented. RESULTS: Five different fenugreek varieties were subjected to a newly developed diosgenin extraction method, and an HPLC chromatogram showed a single peak corresponding to diosgenin. Yield was determined by the standard curve method. Limit of detection (LOD) and limit of quantification (LOQ) for the assay were found to be 0.0312 and 0.102 μg, respectively; tcalculated for slope and other statistical parameters were found to be significant (P value < 0.001) for this method. CONCLUSIONS: We have developed a fast, accurate and low cost method for diosgenin extraction from fenu- greek. Although the authors have studied this method only in fenugreek plants, it could be applied to the extraction of a few other plant secondary metabolites, which will help researchers to save time and effort.

Compound heterozygous ß(+) ß(0) mutation of HBB gene leading to ß-thalassemia major in a Gujarati family - A case study.

ß-Thalassemia is a genetic disease characterized by reduced or non-functionality of ß-globin gene expression, which is caused due to a number of variations and indels (insertions and deletions). In this case study, we have reported a rare occurrence of compound heterozygosity of two different variants, namely, HBBc.92G > C and HBBc.92 + 5G > C in maternal amniotic fluid sample. Prenatal ß-thalassemia mutation detection in fetal DNA was carried out using nucleotide sequencing method. After analysis, the father was found to be heterozygous for HBBc.92G > C (Codon 30 (G > C)) mutation which is ß(0) type and the mother was heterozygous for HBBc.92 + 5G > C (IVS I-5 (G > C)) mutation which is ß(+) type. When amniotic fluid sample was analyzed for ß-globin gene (HBB), we found the occurrence of heterozygous allelic pattern for aforesaid mutations. This compound heterozygous state of fetus sample was considered as ß(+)/ß(0) category of ß thalassemia which was clinically and genotypically interpreted as ß-thalassemia major. Regular blood transfusions are required for the survival of thalassemia major patients hence prenatal diagnosis is imperative for timely patient management. Prenatal diagnosis helps the parents to know the thalassemic status of the fetus and enables an early decision on the pregnancy. In the present study, we have identified compound heterozygosity for ß-thalassemia in the fetus which portrays the importance of prenatal screening.

Whole-Genome Sequencing of Brevundimonas diminuta XGC1, Isolated from a Tuberculosis Patient in Gujarat, India.

We report the draft genome of Brevundimonas diminuta strain XGC1, isolated from a tuberculosis-infected patient in Gujarat, India. This study also reveals that the B. diminuta XGC1 strain has acquired mutation to confer resistance to quinolone drugs.