Dissertation

Mapping the 5' end of the XYLT1 gene in search of genetic and epigenetic causative mutations in Baratela-Scott Syndrome

Sahraoui, Rebecca

2016

Overview

According to the National Institute of Health (NIH) a disease or disorder is categorized as a rare disorder (or orphan disease) when it affects less than 200,000 people within the US in any given year. Genetic disorders are often characterized by mutations or DNA variants in a given gene. The human genome contains approximately twenty to twenty-five thousand genes, making up the “exome” of an individual. With the availability of the “complete sequence” of the human genome, the study of the structure and function, as well as gene interactions has expanded the ability to improve the diagnosis and treatment of genetic disorders. Sanger sequencing is still considered the “gold standard” in molecular diagnostics, and is often used to confirm mutations found with other technologies. Next generation sequencing (NGS), also called massively paralleled sequencing, has given researchers the ability to overcome some of the issues with traditional Sanger sequencing. While the focus for many years has been genomic mutations causing disease, we know now that epigenetics plays a major role not only in disease, but in normal regulation of the human genome. My project is based on the study of the rare genetic disorder Baratela-Scott Syndrome (BSS), a rare autosomal recessive disorder characterized by common phenotypes including skeletal dysplasia, distinct facial features such as a flattened midface and wide nasal bridge, as well as developmental delay with pre-school age, Prior to my joining the laboratory, there was parentally inherited homozygous variant in the XYLT1 gene found in one patient out of a total of 9 in the cohort. Other enrolled patients had either no mutation in XYLT1or only one allele of this gene was found to carry a deleterious mutation. The reference genome at this locus was revealed to be incomplete, and was shown to be resistant to amplification. With the use of molecular techniques, we were eventually able to identify inherited homozygous causative variants in one newly enrolled patient and most importantly, discover parentally inherited XYLT1 CpG methylation (mCpG) in patients carrying a heterozygous mutation. One patient carried two alleles with hypermethylated CpG in the promoter region and exon 1 of the gene.XYLT1 is not an imprinted gene, and controls as well as unaffected siblings do not show any methylation in the 5’end of this gene. Thus we are now able to conclude BSS can be caused by different events affecting the function of the XYLT1 protein: homozygous loss of function mutations (point mutations or InDels), parentally inherited homozygous methylation defects (mCpG) or a combination of mutation and methylation defects inherited through the germline by unaffected heterozygous carrier parents.

• Publisher: ProQuest Dissertations & Theses
• Subject: Developmental biology / Genetics
• ISBN: 1369116055, 9781369116052