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Lipoprotein lipase deficiency/type I hyperlipoproteinemia
Published in William L. Nyhan, Georg F. Hoffmann, Aida I. Al-Aqeel, Bruce A. Barshop, Atlas of Inherited Metabolic Diseases, 2020
Since the patient with the 6 kb deletion, a number of mutations has been identified, a majority of them missense [8, 50–52], but coding for very reduced or absent enzyme activity. A point mutation in exon 5 was found to account for the majority of alleles in the French-Canadian population, where prevalence is the highest in the world [22, 53, 54]. A C-to-T transition at nucleotide 875 led to a change from proline 207 to leucine. Dot blot analysis is available and a restriction site is available for analysis. G188E was common in Europe. Missense mutations have been found in 28 instances. Stop-codons have been produced by five single-base changes. A 3 kb deletion in exon 9 has been reported [55] and two splice site defects have occurred in intron 2 [56, 57]. The majority of missense mutations have been in exon 5, and in exons 4 and 6, areas of considerable homology among lipases. Some mutations have converted hydrophobic residues to less hydrophobic amino acids. Among mutations found in Japanese, a novel complex deletion insertion mediated by repetitive Alu elements led to the elimination of exon 2 [8]. Direct sequencing of the coding region of the LPL gene has detected some 97 percent of those with LPL deficiency. Mutations are also detectable by deletion/duplication analysis.
A Survey of Newer Gene Probing Techniques
Published in Victor A. Bernstam, Pocket Guide to GENE LEVEL DIAGNOSTICS in Clinical Practice, 2019
Some sequences, such as those of the Alu family, display varying density. Alu elements represent the major family of short interspersed repeats (SINEs) in mammalian genomes and, characteristically, there are approximately 106 copies of a 300-bp sequence scattered throughout the human genome approximately every 3 to 4 kb. Alu sequences are frequently interspersed in the human genomeflank anonymous DNA segments harboring yet undisclosed polymorphismsare at least 50-fold less abundant in centromeric heterochromatic regions, whereas other repetitive, tandemly arranged sequences are found there
Epigenetic mechanisms in bone development
Published in Nicholas C. Harvey, Cyrus Cooper, Osteoporosis: a lifecourse epidemiology approach to skeletal health, 2018
Elizabeth M Curtis, Nicholas C Harvey, Cyrus Cooper
At the other end of the lifecourse, the relevance of DNA methylation has been shown in the pathogenesis of osteoporosis; it has been demonstrated that hypomethylation of Alu elements, (interspersed repetitive DNA elements) are associated with lower bone mineral density in postmenopausal women (34). In another study, methylation of SOST in blood samples was increased in osteoporotic patients, and SOST mRNA in bone cells decreased, in a suggested compensatory mechanism in osteoporosis in order to promote bone formation (35).
Investigation of the genetic structure of Kabyle and Chaouia Algerian populations through the polymorphism of Alu insertion markers
Published in Annals of Human Biology, 2019
Hocine Badache, Sami Boussetta, Amel Benammar Elgaaeid, Lotfi Cherni, Houssein Khodjet El-khil
Alu elements are DNA fragments derived from the small cytoplasmic 7SL RNA and classified as short interspersed nuclear elements (SINEs) (Moran et al. 1996). They are a type of Transposable Elements (TEs) that can amplify and insert their copies into new chromosomal locations in the genome. The vast majority of TEs are no longer capable of transposition, due to mutations that could affect transposition machinery, or they are kept inactive by epigenetic mechanisms (Ray and Batzer 2011). Nevertheless, there remain a few families of actively transposing human TEs (Rishishwar et al. 2015). Actually, Alu elements are the most abundant family of polyTEs, followed by L1 and SVA, and make up ∼10% of the total human genome (Lander et al. 2001). The worldwide survey of human populations using these polymorphisms has supported the African origin of modern humans (Stoneking et al. 1997). With unknown biological function, researchers now adopt them as major players in human evolution, as well as useful tools for molecular genetics and forensic applications (Mamedov et al. 2010). These markers have been widely used to assess the degree of genetic relationships between populations and have shown a discriminative ability for geographically distinct populations as well as for neighbouring populations (e.g. Stoneking et al. 1997; Comas et al. 2000; Santovito et al. 2007; Gonzalez-Perez et al. 2010; Cherni et al. 2011; Frigi et al. 2011; Salem et al. 2014; Zanetti et al. 2014).
Deciphering DMET genetic data: comprehensive assessment of Northwestern Han, Tibetan, Uyghur populations and their comparison to eleven 1000 genome populations
Published in Artificial Cells, Nanomedicine, and Biotechnology, 2018
Jiayi Zhang, Huijuan Wang, Geng Niu, Yongkang Liu, Yanxia Wang, Lirong Zhang, Yanrui Pei, Hongli Zhu, Penggao Dai, Chao Chen
CHST5 encodes a protein that catalyzes the transfer of sulphate to position 6 of galactose (Gal), N-acetylgalactosamine (GalNAc), or N-acetylglucosamine (GlcNAc) residues within proteoglycans and sulphation of O-linked sugars of mucin-type acceptors. For rs2641806 and rs2738792, no available study was found in the PubMed database. As such, this study was the first to report the frequencies of these two SNPs in Han, Tibetan and Uyghur. Both rs2641806 and rs2738792 were located in the 5′UTR region of CHST5. Previous studies found that approximately 75% of the human genome is transcribed, and many of these transcripts contain repetitive elements [29]. Repetitive elements are located in the 5′UTR and 3′UTRs of many mRNAs and are major components of long noncoding RNAs (lncRNAs) [30,31]. The expression of lncRNAs has been linked to several human diseases, including cancer and neurological diseases [32,33]. In particular, Alu elements perform molecular functions in mRNAs and some lncRNAs. No study has confirmed the function alterations caused by these two SNPs. Thus, the detailed function of the two SNPs found in our study must be further investigated.
Hemoglobinopathy gone astray—three novel forms of α-thalassemia in Norwegian patients characterized by quantitative real-time PCR and DNA sequencing
Published in Scandinavian Journal of Clinical and Laboratory Investigation, 2021
Runa M. Grimholt, Bente Fjeld, Olav Klingenberg
Large deletions are the most common cause of α-thalassemia. Although the single gene deletion -α3.7 is the most frequent deletion worldwide, a higher number of different double gene deletions than single-gene deletions have been identified. Ninety-five deletions causing α-thalassemia (ranging from 0.2 to 10.0 kb in size) are registered in the IthaGenes database [20], 68 of them covering at least both α-globin genes. Five of the most common double gene deletions (–SEA, –MED, –THAI, –FIL, –(α)20.5) and two of the most common single-gene deletions (–α3.7, –α4.2) are easily detectable with gap-PCR [8], but other deletions will remain undetected by this method. By using our HBA-CNV application based on qPCR and the ΔΔCq method, a previously unknown double gene deletion, designated –(NOR), was first found in three generations of a Norwegian family, all presented with a thalassemic phenotype. Double gene deletions are most frequently a result of non-homologous recombination [43]. Nevertheless, several deletions caused by homologous recombination are described in the literature [44–46]. Recombination between homeologous (partially homologous) Alu elements represent a major form of genetic instability in the human genome leading to deletions and duplications [47]. Sequencing of the breakpoints of –(NOR) showed that both breakpoints are located within Alu elements and an 18 nt homologous sequence occurring at both the 5′ and 3′ regions (Figure 1(B)). This indicates that the deletion is a result of a simple crossover between homeologous Alu elements that are normally ̴13.4 kb apart.