by Jiankang Jin  , Shumei Song  and Jaffer A. Ajani

Received: 30 June 2020;  Published: 16 September 2020;  doi: 10.21926/obm.genet.2003116

Gastric adenocarcinoma (GAC) is among the three most common cancers in the world. The majority of GAC patients are diagnosed in an advanced stage and have a median survival of ~9 months. There are limited effective therapeutic strategies available in the clinic and currently U.S. Food and Drug Administration (FDA) approved immune therapy is programmed death-1 (PD-1) antibodies (e.g. pembrolizumab) but only a few patients seem to benefit. Transformation to cancer occurs when multiple genes and cellular pathways are [...]

by Nagarajan Paramasivam  , Martin Granzow  , Christina Evers  , Katrin Hinderhofer  , Stefan Wiemann  , Claus R. Bartram  , Roland Eils  and Matthias Schlesner

Received: 24 October 2017;  Published: 16 April 2018;  doi: 10.21926/obm.genet.1802017

Background: With genome sequencing entering clinics as a diagnostic tool to detect genetic disorders, there is an increasing need for bioinformatics-based solutions that enable precise causal variant identification in a timely manner. Workflows for the identification of candidate disease-causing variants usually perform the following tasks: i) identification of variants; ii) filtering of variants to remove polymorphisms and technical artifacts; and iii) prioritization of remaining variants to provide a small set of [...]

by Christine Demanche  , Jacques Guillot  and Magali Chabé

Received: 22 February 2019;  Published: 15 May 2019;  doi: 10.21926/obm.genet.1902078

Pneumocystis spp. are a group of fungi that are known for causing opportunistic infections in immunocompromised individuals. It was only at the end of the 20th century that the scientific community challenged the notion of a unique species in the genus Pneumocystis (i.e., Pneumocystis carinii) that drastically changed the understanding of the natural history of pneumocystosis. It is now accepted that the Pneumocystis genus comprises a group of heterogenous fungi having multiple stenoxenic biological entities. These [...]

by Ugo Testa  , Germana Castelli  and Elvira Pelosi

Received: 27 May 2020;  Published: 06 August 2020;  doi: 10.21926/obm.genet.2003114

Cancer is characterized by sequential and progressive genetic and epigenetic alterations in key proto-oncogenes and tumor suppressor genes, which ultimately lead to tumor development. Advances in the technology of analysis of molecular mechanisms have increased the efficiency of clinical management of cancer patients. Recent years have witnessed a progressive development in technologies that enable the detection of specific molecular abnormalities associated with various types of solid tumors in body fluids, a proc [...]

by Fawzy Georges

Received: 21 April 2020;  Published: 13 August 2020;  doi: 10.21926/obm.genet.2003115

The challenges which face the world today can be summed up in a few words: An increasingly congested world with dwindling areas of viable cultivated land and accelerating climate instability. The combined effect of these realities, together with the trend of striving to extend the average human life, puts the world on the path toward future catastrophe. This situation makes it imperative to seek realistic and practical solutions, which must be able to address food shortages and climate problems in a timely manner. [...]

by Stamatia Stai

Received: 27 May 2018;  Published: 06 September 2018;  doi: 10.21926/obm.genet.1803032

Immunoglobin A Nephropathy (IgAN) is the most common primary glomerulonephritis worldwide. Its development is characterized by the deposition of immune complexes that consist of abnormally galactosylated IgA1 molecules and IgG or IgA autoantibodies in the mesangium and the subsequent induction of renal injury. Recent research has shed light to many aspects of the pathogenesis of the disease, including the contribution of epigenetic modifications in its onset and progression. This review aims to present some of the [...]

by Melita Vidakovic  , Jessica Marinello  , Maija Lahtela-Kakkonen  , Daumantas Matulis  , Vaida Linkuvienė  , Benoît Y. Michel  , Ruta Navakauskiene  , Michael S. Christodoulou  , Danielle Passarella  , Saulius Klimasauskas  , Christophe Blanquart  , Muriel Cuendet  , Judit Ovadi  , Stéphane Poulain  , Fabien Fontaine-Vive  , Alain Burger  and Nadine Martinet

Received: 30 May 2018;  Published: 16 August 2018;  doi: 10.21926/obm.genet.1803029

Background: With their varied pharmacophores, natural products are interesting tools to open the drug discovery pipeline. Several plant secondary metabolites are components of the human diet and have reported epigenetic activities. In this study, we screened a small natural compound library for epigenetic activities. Methods: Seventy-one different natural products plus 17 controls collected from all collaborating laboratories were screened. Localized DNA methylation (DNAm) was studied on a stretch of the retinoic a [...]

by Laura Privalle  , Patricia Back  , Apurv Bhargava  , Zach Bishop  , Krystal Cisneros  , Isabelle Coats  , Ine Criel  , Lien Dhondt  , Travis Draughn  , Barb Fowler  , Brad Franklin  , Durba Ghoshal  , Jim Lor  , Jennifer Massengil  , Sofie Moens  , Tyson Mooney  , Dannyel Nelson  , Karolien Peeters  , Sashi Sathischyandra  , Caroline Staut  , Yoonhui Sung  , Ann Tuttle  , Annelies Van Hoecke  , Annelies Van Raemdonck  , Marie-Laure Verdegem  , Steven Verhaeghe  , Shane Walsh  , Ann Wierckx  , Qiang Zhao  and Rozemarijn Dreesen

Received: 11 September 2020;  Published: 02 December 2020;  doi: 10.21926/obm.genet.2004120

Demonstration of the stability of traits newly introduced into a plant genome via genetic engineering approaches comprise a significant portion of the safety assessment that these products undergo prior to receiving the requisite regulatory approvals enabling commercial authorization. Different regions of the world have different regulatory requirements and many ask similar questions from multiple and overlapping perspectives. The entire central dogma, that is stability at the DNA level, mRNA level and protein leve [...]

by Lorraine Cowley  and Mari Jones

Received: 30 December 2019;  Published: 26 April 2020;  doi: 10.21926/obm.genet.2002108

This paper explores views of healthcare professionals (HCPs) in genetics and foetal medicine settings on offering pre-natal diagnosis (PND) for adult onset cancer susceptibility (AOCS) genes. Study participants came from different disciplinary backgrounds and all had considered implications of offering PND for AOCS, directly or indirectly, from professional and personal perspectives. Foetal medicine and genetics teams are accustomed to offering PND with the possibility of terminating an affected foetus on the basis [...]

by Parisa Gazerani

Received: 09 May 2018;  Published: 10 October 2018;  doi: 10.21926/obm.genet.1804040

Interactions between genetic and environmental factors in migraine are well known and can potentially determine an individual’s susceptibility to disease and responsiveness to treatment. Consequently, several epigenetic studies have been conducted to determine if and how genes are activated or inactivated in response to a diverse range of environmental migraine triggers. The results, in turn, have helped elucidate how these factors can promote or inhibit migraine progression or therapeutic response and can guide de [...]

by Walid AL-ACHKAR  , Manar As’sad  , Thomas Liehr  , Adnan Ikhtiar  and Abdulsamad Wafa

Received: 14 August 2018;  Published: 20 June 2019;  doi: 10.21926/obm.genet.1902081

Background: The aggressive T-cell acute lymphoblastic leukemia (T-ALL) is one of the frequently occurring malignancies of the thymocytes. T-ALL is observed in 15% and 25% of all new diagnosed ALL cases in children and adults, respectively. Notably, T-ALL has a 3-fold higher incidence in males than in females. In nearly half of T-ALL cases, structural and/or numerical chromosomal abnormalities are detected, which have an important prognostic significance. A well-known genetic subtype of B-ALL, high hyperdiploidy (He [...]

by Joep Geraedts

Received: 05 June 2018;  Published: 23 July 2018;  doi: 10.21926/obm.genet.1803024

Both preimplantation genetic testing (PGT) and prenatal diagnosis (PND) are powerful tools to tackle the transmission of inherited disorders carried by families from generation to generation. Here, we present an overview of the current landscape of both methods and identify the pros and cons of each of these reproductive options. In prenatal testing, non-invasive diagnostic methods have become available as an alternative for invasive diagnosis. Different genome sequencing strategies have now been introduced that en [...]

by Oyovwi Mega Obukohwo  , Oyelere Abosede Oreoluwa  , Odewale O. Comfort  and Afolabi Opeyemi Olanike

Received: 24 March 2024;  Published: 20 June 2024;  doi: 10.21926/obm.genet.2402246

Infertility affects millions globally, with 10-15% of couples experiencing unexplained cases. Despite advancements in medicine, the cause remains unknown, causing emotional distress. Recent research suggests a genetic basis for this issue. This review aims to provide a better understanding of the underlying genetic factors contributing to unexplained infertility and potentially identify genetic markers that could aid in the diagnosis and treatment of this condition. A literature review was conducted to understand t [...]

by Hagit Daum  , Simcha Yagel  and Mordechai Shohat

Received: 11 March 2019;  Published: 15 May 2019;  doi: 10.21926/obm.genet.1902077

Background: Fetal exome sequencing is becoming a crucial modality for genetic investigation whenever fetal malformations are documented in the context of normal chromosomal microarray analysis (CMA). When ultrasound findings are non-specific, the robustness of exome sequencing may be the only way to achieve a molecular diagnosis during pregnancy. Case: We describe a case of multiple non-specific fetal findings with the eventual diagnosis of fetal Kabuki Syndrome by exome sequencing. Conclusions: This case stresses [...]

by Xinying Hong  and Miao He

Received: 04 May 2022;  Published: 02 August 2022;  doi: 10.21926/obm.genet.2203161

Galactosemia is a group of hereditary disorders of galactose metabolism. Newborn screening for galactosemia type I is mandatory in all states in the US since timely intervention can prevent life-threatening sequela. The biochemical basis, clinical presentation, and potential treatment options for different types of galactosemia are described. This review has a focus on the screening methodologies, including the principle of the assay, the transition from the initial bacteria inhibition test to the modern fluorometr [...]

by Ciro Comparetto  , Florence Dupré  and Franco Borruto

Received: 15 July 2019;  Published: 12 December 2019;  doi: 10.21926/obm.genet.1904101

Background: Clinical or medical genetics deals with the study and diagnosis of genetic diseases. It is oriented to the formulation of the clinical diagnosis of genetic diseases and genetic counseling to evaluate the possible reproductive risk for the patient and his/her family. The geneticists here play a role in the diagnosis and prevention of some of the diseases occurring most frequently, such as cancer and cardiovascular diseases. Methods: State-of-the-art through literature review. Results: Genetic counseling [...]

by Xi Chen  and Jianhua Xuan

Received: 19 October 2019;  Published: 07 April 2020;  doi: 10.21926/obm.genet.2002107

The analysis of gene networks and signalling pathways plays a key role in understanding gene functions, i.e., their effects on the development of a particular disease. Yet, for many heterogeneous diseases, the number of known disease-associated genes is limited. Identifying disease-associated genes is still an open challenge. To understand the functions of genes associated with a disease, we develop a Metropolis-Hastings sampling based SIGnificant NETwork (MSIGNET) identification approach. MSIGNET integrates diseas [...]

by Stefania Policicchio  , Emma L Dempster  and Therese M Murphy

Received: 20 June 2018;  Published: 06 October 2018;  doi: 10.21926/obm.genet.1804039

Suicide is the second leading cause of death globally among young people and the tenth leading cause of death across all ages. Approximately 800,000 people die by suicide every year representing a significant global health burden. Despite this burden, the molecular pathology of suicide remains poorly understood. A number of recent studies have shown that epigenetic alterations are associated with suicidal behaviour. These epigenetic mechanisms, which act to regulate gene expression via modifications to DNA, histone [...]

by Anne-Marie Laberge  and Wylie Burke

Received: 30 July 2017;  Published: 21 September 2017;  doi: 10.21926/obm.genet.1703006

Genetic screening is the process of systematically evaluating a defined population for genetic conditions or predispositions, in the hope of providing benefit to those with a positive result. With advances in sequencing technology, genetic screening is moving from phenotype-based to genotype-based testing. Although sequencing technology offers expanded opportunities for early identification of disease, the availability of a suitable and acceptable test is not a sufficient justification to proceed: established crite [...]

by Luis Delaye

Received: 05 May 2019;  Published: 11 July 2019;  doi: 10.21926/obm.genet.1903083

Background: Phylogenetic analysis shows that Pneumocystis have coevolved with their mammalian hosts for millions of years. As a result, infection by Pneumocystis is species specific (i.e. a given Pneumocystis species can infect only a single species of host). This specificity suggests the existence of a Red-Queen dynamic between Pneumocystis and its host. Evidence of this dynamic is provided by the molecular diversity and the elevated rate of non-synonymous versus synonymous (dN/dS) codon substitutions among Pneumo [...]

by Rita Payan-Carreira

Received: 30 December 2018;  Published: 29 April 2019;  doi: 10.21926/obm.genet.1902074

In a mammal, at the beginning of its development, the gonad is bipotential. The shift into a male or female pathway is coordinated by the sex chromosomal complement, which triggers a series of genetic pathways signaling the developmental pattern of the gonadal anlage. Being mutually exclusive, the differentiated gonad should be either a testis or an ovary. In females, the absence of SRY, a testis-determining gene, drives the signaling cascades controlling the ovarian differentiation. Albeit rare, disorders of the g [...]

by Masahiro Sato  , Issei Saito  , Eri Akasaka  and Emi Inada

Received: 11 October 2020;  Published: 10 March 2021;  doi: 10.21926/obm.genet.2101126

Direct colony cloning of adherent mammalian cells using rings or dilution cloning has been used frequently for obtaining stable transfectants after gene delivery. As an alternative to these methods, successful isolation of the cells in a single colony is possible by placing a trypsin-immersed small paper disk onto the colony and subsequently picking up the paper with the assumption that it carries the trypsinized cells. However, the cloning success using this technique largely relies on the cell type used. In the p [...]

by Ayub Nor Hanin  , Mat Yunus Abdul Masani  , Ong-Abdullah Janna  , Omar Abdul Rasid  and Ghulam Kadir Ahmad Parveez

Received: 18 December 2024;  Published: 15 April 2025;  doi: 10.21926/obm.genet.2502292

Oil palm is the most productive vegetable oil crop compared to other oil-bearing crops because it produces the highest oil yield per hectare. Palm oil is very versatile since it is used for producing food and beverages, personal care and cosmetics, cleaning products, biofuel, and bioenergy. To cater to the increasing demand in the global palm oil market, much research has been done to improve the oil's yield and modify its quality in addition to the oil palm height through breeding. Due to its long breeding cyc [...]

by Diane B. Paul

Received: 29 March 2021;  Published: 14 May 2021;  doi: 10.21926/obm.genet.2102130

This article explores difficulties encountered by those with no personal experience of a chronic disease or disability in accurately evaluating the quality of life with a condition present from birth. In most countries, cost-effectiveness analysis relies on ratings of health states by members of the general population, who must try to imagine what life for those affected is like based on (usually brief) descriptions of the conditions. That task is challenging for reasons that have been well-discussed in the literat [...]

by Mariette Kokolo  and Montse Bach-Elias

Received: 25 June 2020;  Published: 16 November 2020;  doi: 10.21926/obm.genet.2004118

Non-coding RNAs (ncRNAs) have emerged as one of the most abundant regulatory molecules. However, their roles and functions are significantly different from those of proteins. Moreover, around 95% of the human genome contains non-coding DNA. ncRNAs contribute by far the majority of human transcriptional units, and the functions of the most are yet unknown. Here, we highlight that an important RNA sequence region, encompassing an exon-intron hairpin loop (also called IDX-rasISS1), of the H-Ras pre-mRNA may encode an [...]

by Laurence Pougnet  , Gilles Nevez  and Solène Le Gal

Received: 17 December 2018;  Published: 22 May 2019;  doi: 10.21926/obm.genet.1902080

Pneumocystis pneumonia (PCP) is the most frequent AIDS-defining disease among HIV-infected individuals in developed countries, and also affects immunocompromised non-HIV patients. Experimental studies on rodent models carried out in the early eighties have shown that Pneumocystis spp. can be transmitted via the airborne route. Unfortunately, this mode of acquisition and transmission has long been overlooked by physicians because PCP in immunosuppressed patients was considered to result from reactivation of a latent [...]

by Mary J. Lotesto  and Stacey L. Raimondi

Received: 26 June 2020;  Published: 07 October 2020;  doi: 10.21926/obm.genet.2004117

Estrogen-based cancers affect a substantial portion of the female population in the United States. While multiple studies have examined the effect of estrogen receptor alpha (ERα/ESR1) in cancer, the effects of ERβ/ESR2 are not as well understood in tumor tissues. Furthermore, there are few studies examining the role of specific binding partners of the estrogen receptors, such as early B-cell factor 1 (EBF1). EBF1 has been shown to have a role in B cell development and differentiation and is also know [...]

by Niccolo Caldararo

Received: 19 October 2021;  Published: 11 January 2022;  doi: 10.21926/obm.genet.2201145

The evolution of hominins, members of the zoological tribe Hominini, has been a much-studied topic, and the construction of phylogenetic trees has been the key method in molecular evolutionary studies. How scientists determine the phylogenetic trees are governed by the assumptions they place on the construction of similarities and differences in morphological traits, the differences in the number of base pairs in the genomes, and the number of similar gene clusters that code for traits (haplotypes) or are error seq [...]

by Virginie Vignard  and Delphine Fradin

Received: 13 March 2018;  Published: 15 May 2018;  doi: 10.21926/obm.genet.1802020

Melanoma is a highly aggressive skin cancer with high incidence worldwide. There is growing evidence that aberrantly expressed non-coding RNAs (ncRNAs) play a role in the development, progression and dissemination of melanoma tumor cells. Among the many types of ncRNAs described in this review, the functions of micro- and long non-coding RNAs are described and related to the six hallmarks of cancer. Recently, ncRNAs discovered in body fluids have become known as one of the most promising groups of oncological bioma [...]

by Ameya Patil  , William E Sweeney  and Ellis D. Avner

Received: 07 August 2018;  Published: 23 December 2018;  doi: 10.21926/obm.genet.1804056

Renal cysts are present in a wide variety of hereditary renal diseases in children. The term polycystic kidney disease (PKD) refers to two specific hereditary diseases, distinguished by the usual age of onset and genetic cause: autosomal recessive polycystic kidney disease/congenital hepatic fibrosis (ARPKD/CHF, MIM *606702) and autosomal dominant polycystic disease (ADPKD-OMIM *601313 and OMIM *173910). ARPKD/CHF is characterized by cystic dilations of the renal collecting ducts and developmental defects of biliar [...]

by Kwang Poo Chang  , Dennis K.P. Ng  , Chia-Kwung Fan  , Ramesh B. Batchu  and Bala K. Kolli

Received: 29 December 2019;  Published: 24 February 2020;  doi: 10.21926/obm.genet.2001103

The parasitic protozoa in the genus of Leishmania have exceptionally favorable attributes for exploitation as a vehicle for safe and effective delivery of transgenically incorporated vaccines against infectious and malignant diseases. A dual suicidal mechanism was installed in Leishmania via genetic and chemical engineering in vitro for accumulation of photosensitizers, rendering them sensitive to dim light for inactivation. Leishmania so inactivated are non-viable, but immunologically competent to deliver vaccines [...]

by Rie Sasaki  , Hiroto Ito  and Masami Okamoto

Received: 01 March 2022;  Published: 14 June 2022;  doi: 10.21926/obm.genet.2202155

In this study, we examined the effect of a combination of surface topographies (fiber alignments) and different stiffness of poly(L-lactic acid) (PLLA) substrates on the direct relationship between anti-cancer drug (CDDP) sensitivity for MDA-MB-231 cells and mesenchymal properties under both normal and hypoxic conditions. In addition, we studied the induction of epithelial–mesenchymal transition (EMT). The CDDP treatment under hypoxia indicated poor adhesion of MDA-MB-231 cells as well as significant repression of [...]

by Ute Moog  and Domenico Coviello

Received: 14 August 2018;  Published: 13 September 2018;  doi: 10.21926/obm.genet.1803034

he publication of the double helix DNA structure in 1953 [1] was the kick-off of numerous efforts to understand and unravel the complexity of the human genome. It took 50 years until the human genome project, based on Sanger sequencing, was completed in 2003 [2]. This was followed by what may be considered a revolution in the field of DNA analysis: the introduction of Next Generation Sequencing (NGS) in 2005 consisting of massively parallel sequencing of DNA fragments which allows the high throughput analysis of la [...]

by Ilaria Scarpelli  , Fabienne Marcelli  , Francesca Mattioli  and Jacqueline Schoumans

Received: 01 April 2019;  Published: 09 August 2019;  doi: 10.21926/obm.genet.1903088

With the advent of next-generation sequencing (NGS), genomic profiling of tumors has been gradually introduced into the clinical setting and has become a standard in cancer care. NGS allows convenient, rapid, and inexpensive sequencing and the commercially available NGS panels enable the detection of single or global genomic alterations of germline and somatic origin. Today, genomic mutation profiling using NGS is indispensable for disease evaluation and prediction of prognosis or responsiveness to cancer therapy. [...]

by Arpitha Shankar Bandi  and Prashant Kaushik

Received: 22 March 2022;  Published: 23 May 2022;  doi: 10.21926/obm.genet.2202154

India is home to several medicinal herbs including turmeric. Turmeric is one of the major produces of India, primarily due to its unique and valuable medicinal and therapeutic properties. However, the growth and yield of turmeric are greatly affected by salt stress in certain parts of the country, especially those near water bodies where significant yield losses have been reported. To mitigate these losses caused by salt stress, certain plant breeding methods, transgenic approaches, and candidate genes along with i [...]

by Tobias Geis  , Ute Hehr  , Roland Brandl  , Saskia Herbst  , Hugo Segerer  , Michael Melter  and Sophie Hinreiner

Received: 31 August 2017;  Published: 06 March 2018;  doi: 10.21926/obm.genet.1801015

Background: Neonatal muscular hypotonia is a common clinical feature on neonatal intensive care units with a broad spectrum of etiologies. Besides more common and obvious underlying conditions like prematurity or Down syndrome many rare disorders with often poor prognosis need to be considered. Congenital brain malformations detected on ultrasound or/and magnetic resonance imaging might constitute the clinical hallmark in differential diagnosis. We report on our approach combining cerebral imaging and application o [...]

by Bhanuka Maheshwara Sisira Kumara Pahala Ralalage  , Nirmani Kaluarachchi  , Malshani Randunu  , Munshifa Jainulabdeen  , Rohini Nanthakumar  , Sameera Vishwakula  and B. Prasanna Galhena

Received: 01 October 2022;  Published: 06 February 2023;  doi: 10.21926/obm.genet.2301177

Fluorescence In-Situ hybridization (FISH) is a sensitive and highly efficient technique commonly used in routine diagnostics. Most of these tests that use analyte-specific reagents are not approved by US Food and Drug Administration (FDA) but are developed by individual test laboratories. There is an emerging demand for prenatal diagnosis of aneuploidies by FISH. Since most of these assays are laboratory-developed tests, it is essential to validate them prior to their use in diagnosis. However, validation procedure [...]

by Joun Park  , Xianzun Tao  and R. Grace Zhai

Received: 13 January 2020;  Published: 20 March 2020;  doi: 10.21926/obm.genet.2001106

By adjusting gene expression in response to environmental changes, cells can optimize fitness as needed. Alternative splicing is one of the most important post-transcriptional regulation steps, broadly involved in diverse physiological and pathological conditions. Here, we present 5 cases of alternative splicing conferring increased neuroprotection through diverse mechanisms. These examples highlight the enormous power of alternative splicing in maintaining viability of neurons. From pre-mRNA secondary structure al [...]

by Xuhua Xia

Received: 09 June 2019;  Published: 17 October 2019;  doi: 10.21926/obm.genet.1904097

Phage as an anti-bacterial agent must be efficient in killing bacteria, and consequently needs to replicate efficiently. Protein production is a limiting step in replication in almost all forms of life, including phages. Efficient protein production depends on the efficiency of translation initiation, elongation and termination, with translation initiation often being rate limiting. Initiation signals such as Shine-Dalgarno (SD) sequences and start codon are decoded by anti-SD sequences and initiation tRNA, respect [...]

by Johanne Traeger-Synodinos  and François Rousseau

Received: 06 September 2019;  Published: 11 September 2019;  doi: 10.21926/obm.genet.1903094

We present here the content and articles of this special issue on genetic screening, putting them in perspective with the field and between themselves.

by Ivan Y. Iourov  , Ilia V. Soloviev  , Yuri B. Yurov  and Svetlana G. Vorsanova

Received: 02 February 2019;  Published: 20 March 2019;  doi: 10.21926/obm.genet.1901067

Fluorescence in situ hybridization (FISH) seems to be the most applicable and versatile molecular cytogenetic platform for visual interphase chromosome analysis offering a variety of opportunities for studying chromosomal structure and behaviour at the highest microscopic resolution and at all stages of the cell cycle. Quantitative assessment of FISH results has been repeatedly shown to increase the efficiency of FISH-based approaches. Here, we explore the potential of interphase quantitative FISH (IQ-FISH), which [...]

by Ivan Y. Iourov  , Svetlana G. Vorsanova  and Yuri B. Yurov

Received: 29 May 2018;  Published: 15 August 2018;  doi: 10.21926/obm.genet.1803028

Runs of homozygosity (ROH) are uninterrupted contiguous regions within the genome exhibiting allelic homozygosity (alleles are inherited from the same parent). Genome-wide analyses consistently demonstrate that megabase-scale ROH are ubiquitous in humans, reflecting individual demographic history. The number and length of ROH correlate increasingly with the degree of consanguinity and can be associated with genetic diseases in both inbred and outbred individuals. Genomic imprinting and uniparental disomy (UPD) are [...]

by Giuseppe Cocco  and Philipp Amiet

Received: 23 March 2021;  Published: 30 July 2021;  doi: 10.21926/obm.genet.2103133

“Epigenetics is the study of how your behaviors and environment can cause changes that affect the way your genes work. Unlike genetic changes, epigenetic changes are reversible and do not change your DNA sequence, but they can change how your body reads a DNA sequence” (https://www.cdc.gov/genomics/disease/epigenetics.htm). Epigenetic interactions, along with the genetic expression in innate cells, change the structure and function of chromatin, and thus, turn the genes on and off. Epigenetic changes influence dise [...]

by Yuri Shavrukov

Received: 03 March 2020;  Published: 04 March 2020;  doi: 10.21926/obm.genet.2001104

by Khue Vu Nguyen

Received: 18 January 2018;  Published: 31 January 2018;  doi: 10.21926/obm.genet.1801012

With the increasing ability to control infectious and nutritional diseases in developed countries, there has come the realization that genetic and epigenetic regulation in diseases are a major cause of disability, death, and human tragedy. Here, I discuss current knowledge about this matter including the diagnosis, counseling, treatment and management as well as some current therapeutic interventions such as gene, stem cell, epigenetic therapies and future directions in the field.

by Svetlana G. Vorsanova  , Yuri B. Yurov  , Ilia V Soloviev  , Alexei D Kolotii  , Irina A Demidova  , Viktor S Kravets  , Oxana S Kurinnaia  , Maria A Zelenova  and Ivan Y. Iourov

Received: 08 February 2019;  Published: 20 March 2019;  doi: 10.21926/obm.genet.1901068

Recently, numerous studies have reported convincing data suggesting that chromosome instability may be not only a trigger of cancers but a possible mechanism for a wide spectrum of brain diseases. According to our original experience, chromosome instability is commonly observed during karyotyping of children with neuropsychiatric diseases and congenital malformations. To understand mechanisms of non-cancerous diseases potentially mediated by chromosome instability, which may represent an important target for molecu [...]

by Samson Adedeji Adejumo  , Angus Nnamdi Oli  , Adekunle Babajide Rowaiye  , Nwamaka Henrietta Igbokwe  , Chinelo Kene Ezejiegu  and Zwanden Sule Yahaya

Received: 11 April 2023;  Published: 11 December 2023;  doi: 10.21926/obm.genet.2304206

Over the past few decades, probiotics have emerged as a viable medical tool for preventing and/or treating diseases. This narrative review provides recent findings on Probiotics and their benefits on the host immune system. It also highlights the specific mechanisms through which probiotics mediate those benefits. The study also explores the topical or systemic probiotic administration method. Authors screened databases like Google Scholar, Web of Science, PubMed, Scopus, and China National Knowledge Infrastructure [...]

by Thomas Liehr  , Monika Ziegler  , Nadezda Kosyakova  and Ahmed B.H. Al-Rikabi

Received: 16 March 2018;  Published: 17 May 2018;  doi: 10.21926/obm.genet.1802021

Background:Fluorescence in situ hybridization (FISH) can be performed on metaphase- and/or interphase cells. Metaphase cells can exclusively be obtained and studied after time-consuming cell culture. Therefore, this technique is suitable only for cells derived from peripheral blood, bone marrow or fibroblasts, the latter including skin, tumour or "prenatal tissues", such as the amnion or chorion. On the other hand, interphase cells can be gained from many different cells and even without cell culture. Methods:Here, [...]

by Whitney Rabacal  , Emily Rayens  and Karen Norris

Received: 02 November 2018;  Published: 27 December 2018;  doi: 10.21926/obm.genet.1804057

Pneumocystis causes life-threatening pneumonia in immunocompromised populations. More recently it has been implicated as a co-factor in a number of chronic lung diseases including chronic obstructive pulmonary disease (COPD), severe asthma, and cystic fibrosis (CF). In this review, we will examine the current literature regarding Pneumocystis and lung diseases in the HIV-infected patients and non-HIV immunocompromised populations, and the barriers to prophylaxis and treatment in these patients. Trimethoprim sulfame [...]

by Michelle A. Camarata  , Uyen To  and Michael L. Schilsky

Received: 18 July 2018;  Published: 22 August 2018;  doi: 10.21926/obm.genet.1803030

Wilson Disease is a monogenetic disorder of copper metabolism affecting the ATP7B gene. Treatment is lifelong and focuses on removal of copper to arrest disease progression and improve the clinical manifestations of copper toxicity. Currently the only cure is liver transplantation, however, lifelong monitoring and immunosuppressive medications are still needed afterwards. The possibility of introducing functional ATP7B gene through gene therapy provides an exciting potential option for achieving a more permanent cu [...]

by Albena Staynova  , Ljubomira Hadjiiska  , Valeria Hadjidekova  and Rositsa Hristova

Received: 14 August 2018;  Published: 22 October 2018;  doi: 10.21926/obm.genet.1804043

Background: The purpose of study was to assess the cytogenetic effect of chronic low dose radiation exposure of nuclear power plant workers using the micronucleus centromere assay. This method allows the differentiation between centromere-positive micronuclei containing whole chromosome and centromere-negative micronuclei containing acentric fragment pointing to clastogenic action of ionizing radiation. Methods: The effect of low dose occupational exposure was estimated in 32 nuclear power plant workers using in si [...]

by Konstantinos Magganas  , Sophia Delicou  , Aikaterini Xydaki  and Zoi Pallantza

Received: 19 May 2019;  Published: 17 September 2019;  doi: 10.21926/obm.genet.1903095

Thalassemia syndromes are a group of hemoglobinopathies characterized by gene defects that disrupt normal hemoglobin production. Thalassemia intermedia (TI) is referred to as a group of disorders with a less severe form of the disease compared to thalassemia major. We present a case of a 60-year-old woman who was referred to a hematologist for chronic anemia and splenomegaly.

by Mohamed Zaiou

Received: 16 March 2020;  Published: 17 March 2020;  doi: 10.21926/obm.genet.2001105

by Camila Sandoval  , Colleen A Lambo  and Michael Carey Satterfield

Received: 01 June 2018;  Published: 28 December 2018;  doi: 10.21926/obm.genet.1804058

Understanding the pathophysiology of disease can be an essential step to determining where and how to intervene for preventive or corrective health. Intrauterine growth restriction (IUGR) has been defined in livestock species as impaired gestational development of a fetus or its parts [1]. This broad category of ailments described by low fetal weight is accompanied by susceptibility to adult onset of chronic disease through fetal programming of numerous organ systems and their functions. This concern affects humans [...]

by Susana Ruiz-Ruiz  , Carolina A Ponce  , Nicole Pesantes  , Rebeca Bustamante  , Gianna Gatti  , Viviana San Martin  , Mireya Gutierrez  , Mariana Izquierdo  , Sergio L Vargas  , Fabien Magne  and Vicente Pérez-Brocal

Received: 30 January 2019;  Published: 18 March 2019;  doi: 10.21926/obm.genet.1901066

Background: Pneumocystis jirovecii colonization in patients is associated with a low organism burden, which supports the need to use highly sensitive molecular techniques, such as nested-PCR to determine the presence of the organism. However, few studies have considered the effect of nucleic acid extraction methods on the detection of P. jirovecii. Here, we evaluate how pre-treatment affects microbial detection. Methods: Lung tissue samples from fifteen autopsied infants were processed using two different DNA extra [...]

by Tahereh Fatemian  and Ezharul Hoque Chowdhury

Received: 29 March 2019;  Published: 15 August 2019;  doi: 10.21926/obm.genet.1903090

Introduction of biocompatible ingredients into nano-material formulations has been studied as a strategy for the enhancement of the pharmacokinetics as well as pharmacodynamics of the final product. With the aim of enhancing drug loading and the ultimate efficacy, incorporation of Bovine Serum Albumin (BSA) into carbonate apatite (CA) nanoparticles structure was employed in the present study. As a result of BSA embedding in the CA formulation, approximately three-times higher loading efficiency was achieved for pac [...]

by Sylvie Langlois  and R Douglas Wilson

Received: 01 August 2017;  Published: 26 September 2017;  doi: 10.21926/obm.genet.1703007

Prenatal genetic aneuploidy screening approaches are designed to identify pregnant patients at increased risk of having a fetus affected. Conventional prenatal screening has consisted in providing women a risk estimate of having a pregnancy affected with trisomy 21 or trisomy 18 based on maternal age and analysis of serum markers and ultrasound nuchal translucency (NT) measurement. In 2011, the introduction of cell-free DNA (cfDNA) based screening into clinical practice has provided new options for aneuploidy scree [...]

by Frenny Sheth  , Thomas Liehr  , Kristin Mrasek  , Joris Andrieux  , Stuti Tewari  , Naznin Lubna  and Jayesh Sheth

Received: 23 March 2018;  Published: 07 September 2018;  doi: 10.21926/obm.genet.1803033

Background: Small supernumerary marker chromosomes (sSMC) are rare cytogenetic findings in general, but especially in Turner syndrome so called sSMCT in a karyotype 46, X, +mar are even more scarce. According to the literature, sSMCT are derived from one of the Y-chromosomes in ~70% of the cases. Thus, to identify the presence of Y-chromosomal material is imperative, since these cases have an increased risk of gonadoblastoma deriving from the streak gonads. Methods: A 24-year-old short statured male presented with [...]

by M. Robyn Andersen  , Kelsey Afdem  , Marcia Gaul  , Shelly Hager  , Erin Sweet  and Leanna J. Standish

Received: 27 February 2019;  Published: 26 July 2019;  doi: 10.21926/obm.genet.1903087

Patients’ lay theories about the cause of their cancer may influence patient behavior and adjustment, they have also been found to differ substantially from scientific evidence of cancer risk factors. This report describes beliefs about genetic causes of breast cancer, among 522 recently diagnosed breast cancer survivors participating in an observational study. Patients were asked to respond to an open-ended question about the cause of their cancer. Causes mentioned included family history, genetics, lifestyl [...]

by Racha El-Hajj Ghaoui  , Dorothy Hung  and Bhavna Padhye

Received: 24 December 2018;  Published: 17 April 2019;  doi: 10.21926/obm.genet.1902073

Hypodiploidy has a low incidence in childhood acute lymphoblastic leukaemia (ALL). Patients are usually stratified into three subgroups, to allocate the correct treatment according to their ploidy level: high hypodiploidy (40-45 chromosomes), low hypodiploidy (33-39 chromosomes) and near haploidy (23-29 chromosomes). In this paper, a case is presented of near-haploid childhood ALL where fluorescence in situ hybridisation (FISH) provided an insight into the near-haploidy chromosomal aberration initially missed on ro [...]

by Annapaola Mariniello  and Silvia Novello

Received: 15 November 2018;  Published: 22 March 2019;  doi: 10.21926/obm.genet.1901069

Immune oncology treatment with immune checkpoint inhibitors (ICIs) is revolutionizing therapeutic approach for advanced non-small cell lung cancer (NSCLC) patients, in terms of longer survival and improved quality of life. To date, the widely used and approved biomarker is programmed death ligand 1 (PD-L1) expression on tumour cells, but it is considered not accurate and it is more likely that many factors, related to both cancer and host, may better predict response to ICI. Among those factors, great attention is [...]

by Maud Gits-Muselli  , Stéphane Bretagne  and Alexandre Alanio

Received: 04 December 2018;  Published: 17 January 2019;  doi: 10.21926/obm.genet.1901060

Pneumocystis jirovecii is an atypical fungus transmitted via the airborne route between humans. This fungus is exclusively associated with humans and almost each individual has encountered it at least once before reaching the age of two. P. jirovecii can be cleared and spontaneously resolutive in immunocompetent, whereas it can be responsible for severe Pneumocystis pneumonia (PCP) in immunocompromised patients. In the next decades, the putative increase of the population of immunocompromised patients is likely to [...]

by Elham Amjad  , Babak Sokouti  , Solmaz Asnaashari  and Siavoush Dastmalchi

Received: 29 August 2024;  Published: 17 December 2024;  doi: 10.21926/obm.genet.2404275

This systematic review examines the role of SnRK2 (Sucrose non-fermenting 1-Related protein Kinase 2) genes in Arabidopsis thaliana growth and responses to abiotic stresses. SnRK2 protein kinases are key components of abscisic acid (ABA) signaling and osmotic stress responses in plants. The review synthesizes findings from numerous studies on how different SnRK2 genes regulate Arabidopsis growth, development, and stress tolerance at various life stages. Key topics covered include SnRK2 functions under environmental [...]

by Ron Hochstenbach  , Martin Poot  and Thomas Liehr

Received: 15 November 2016;  Published: 10 February 2017;  doi: 10.21926/obm.genet.1701002

Small supernumerary marker chromosomes (sSMCs) are centric chromosome fragments additionally present in an otherwise normal human chromosome set that cannot be characterized by classical cytogenetic techniques alone. The majority of sSMCs are not yet related to a defined clinical phenotype. We compiled from the literature all 78 cases with multiple sSMCs per cell in which the chromosomal origin of the sSMCs has been identified. The number of sSMCs varies from 2 to 7; 64% have 2 sSMCs, 14% have 3 sSMCs, and the freq [...]

by Kazuki Mochizuki  , Ayumi Osaki  , Yuko Inamochi  and Toshinao Goda

Received: 18 December 2017;  Published: 30 October 2018;  doi: 10.21926/obm.genet.1804046

Background: Histone modifications, including acetylation and H3 lysine 4 (K4) methylation, are thought to be associated with transcriptional activation during differentiation. Methods: mRNA and histone modifications around the sucrase-isomaltase (SI) gene in Caco-2 cells (a small intestine cell line) during differentiation were determined by qRT-PCR and chromatin immunoprecipitation, respectively. Results: Mono-, di-, and tri-methylation of histone H3K4 on the SI gene correlated with the induction of SI gene expres [...]

by Walter Hughes

Received: 12 September 2018;  Published: 06 December 2018;  doi: 10.21926/obm.genet.1804052

My experiences with the identification and development of the anti-Pneumocystis drugs trimethoprim-sulfamethoxazole, dapsone and atovaquone are recounted. Attention is drawn to certain often-overlooked aspects of these drugs, including their concomitant effects against infections other than Pneumocystis, matters of dosing and adverse effects. During the past four decades several million people worldwide received chemoprophylaxis and treatment with these drugs for Pneumocystis jirovecii pneumonia. The population of [...]

by Joep Geraedts

Received: 08 April 2019;  Published: 14 August 2019;  doi: 10.21926/obm.genet.1903089

Mitochondrial diseases are among the most prevalent inborn errors of metabolism. The overwhelming majority of mitochondrial diseases (about 85%) result from mutations in nuclear genes involved in oxidative phosphorylation, while some (15%) are caused by mutations in mitochondrial DNA (MtDNA). The familial mtDNA mutations are exclusively inherited from the mother. There are four main methods available to prevent the transmission of mtDNA mutations: preimplantation genetic diagnosis (PGD) or prenatal diagnosis (PND) [...]

by Faten Dhawi

Received: 20 February 2024;  Published: 20 May 2024;  doi: 10.21926/obm.genet.2402235

Pearl millet (Pennisetum glaucum), a vital cereal crop renowned for its drought tolerance, is a cornerstone for smallholder farmers in arid and semi-arid regions, ranking as the fifth most significant cereal globally. Despite its resilience, the molecular mechanisms underlying its tolerance to heat stress remained elusive. To address this knowledge gap, we subjected ten-day-old pearl millet seedlings to an unprecedented temperature of 50°C for 60 seconds. Subsequent next-generation RNA sequencing aimed to unrav [...]

by Irina L. Puppo  , Ziravard N. Tonyan  , Alisa N. Panina  , Ksenia V. Shunkina  , Alsu F. Saifitdinova  , Yulia A. Loginova  , Anna A. Kinunen  , Julia R. Pastuhova  , Olga A. Leonteva  , Olga G. Chiryaeva  , Olga V. Malysheva  , Elena M. Fedorova  , Tatyana V. Vavilova  and Natalia K. Bichevaya

Received: 28 March 2022;  Published: 22 June 2022;  doi: 10.21926/obm.genet.2202157

Robertsonian translocations (RTs) are very common balanced structural chromosome rearrangements in humans. Due to alterations in the chromosome segregation pattern and the formation of unbalanced gametes and embryos, the carriers of RTs have a significant risk of reproductive failure. For over 30 years, fluorescent in situ hybridization (FISH) has been used for preimplantation genetic testing for chromosomal structural rearrangement (PGT-SR) in carriers of RTs. The data obtained by performing FISH for PGT-SR can be [...]

by Selin Galatalı  , Damla Ekin Özkaya  , Taner Mercan  and Ergun Kaya

Received: 27 July 2023;  Published: 19 October 2023;  doi: 10.21926/obm.genet.2304198

In the face of rapid population growth worldwide, humanity's need for plant and animal products is increasing. In this regard, the organizations in charge of production make production and consumption forecasts for the future and try to accelerate the work aimed at increasing production. There are various ways of increasing production. The first of these is the improvement of cultivation techniques, the expansion of irrigated agricultural areas, and the effective control of diseases and pests. The second is to find [...]

by Martina C Cornel

Received: 13 July 2017;  Published: 11 February 2018;  doi: 10.21926/obm.genet.1801013

Technology makes it possible to expand many of the current screening programs. Initiatives for preconception screening of carrier status of recessive diseases, prenatal screening of aneuploidies and neonatal screening were initially undertaken by targeting one or at most, a few, conditions. Tandem mass spectrometry and genomic technologies, such as sequencing and panel testing, make it possible to increase the scope of these programs to include more disorders or markers. While inclusion of a larger number of condit [...]

by Zheng Zuo

Received: 01 February 2021;  Published: 16 August 2021;  doi: 10.21926/obm.genet.2103134

The methylation effects on protein-DNA interactions, which can be perceived as a special kind of specificity of transcription factors, have been successfully quantified in the last years by various methods. In this work, I give a summary about the sequence encoding scheme, the underlying additive model about specificity and methylation sensitivity, and the regression strategy to analyze Methyl-Spec-seq data. Then I explain why given the current experimental setup, it is more appropriate to model the methylation eff [...]

by Melania Formisano  and Giandomenico Corrado

Received: 11 June 2019;  Published: 23 July 2019;  doi: 10.21926/obm.genet.1903086

Background: DNA typing has revolutionized not only diagnostics and forensics but also how we can analyze food. A number of techniques have been successfully applied for DNA analysis of plant-derived food. However, unlike forensics, a universally employed method has not yet emerged. Methods: A keyword-based search was performed using the ISI-Web of Science database to look for research articles on DNA testing in agri-food chain. After screening and eligibility check, a Systematic Review was compiled focusing on the [...]

by Yuri B. Yurov  , Svetlana G. Vorsanova  and Ivan Y. Iourov

Received: 06 February 2019;  Published: 30 April 2019;  doi: 10.21926/obm.genet.1902076

The human brain has been repeatedly shown to exhibit intercellular/somatic genomic variations at the chromosomal level, which are involved in the neuronal diversity in health and disease. Brain-specific chromosomal mosaicism (aneuploidy) and chromosome instability play a role in the normal and pathological neurodevelopment, neurodegeneration and aging of the central nervous system. Regardless of achievements in somatic cell (single-cell) genomics, there is still no consensus on the amounts of chromosomally abnormal [...]

by Siamak Shirani Bidabadi  , Parisa Sharifi  and S. Mohan Jain

Received: 09 June 2021;  Published: 15 September 2021;  doi: 10.21926/obm.genet.2103137

Plant breeding programs have used conventional breeding methods, such as hybridization, induced mutations, and other methods to manipulate the plant genome within the species' natural genetic boundaries to improve crop varieties. However, repeatedly using conventional breeding methods might lead to the erosion of the gene reservoir, thereby rendering crops vulnerable to environmental stresses and hampering future progress in crop production, food and nutritional security, and socio-economic benefits. Integrating in [...]