Human Genetics and Genomics A Practical Guide PDF

Cover
About the Authors
Introduction
1 Exploring Online Genetics Sources
Background
Human Genome Project
National Center for Biotechnology Information (NCBI)
UCSC Genome Browser
The Encyclopedia of DNA Elements (ENCODE)
Roadmap Epigenomic Project
References
Exercise Questions
Additional Exercise Questions
2 Observation of Human Inheritance
Background
Mendelian Genetics
The Transmission of Hereditary Characteristics
Mendelian Disorders
References
Exercise Questions
Additional Exercise Questions
3 Reading, Understanding, and Constructing Human Pedigrees
Background
Basic Pedigree Nomenclature
Modes of Inheritance
Autosomal Recessive Inheritance
Pedigrees Representing Autosomal Recessive Inheritance
Autosomal Dominant Inheritance
Pedigrees Representing Autosomal Dominant Inheritance
X-Linked Recessive Inheritance
Pedigrees Representing X-Linked Recessive Inheritance
X-Linked Dominant Inheritance
Pedigrees Representing X-Linked Dominant Inheritance
Y-Linked Inheritance
Pedigrees Representing Y-Linked Inheritance
Non-Mendelian Patterns of Inheritance
Confounding Factors in Pedigree Generation and
Interpretation
References
Exercise Questions
Additional Exercise Questions
4 Cytogenetics
Background
Generation of Karyograms/Chromosome Banding
FISH, Fluorescent In Situ Hybridization
Comparative Genomic Hybridization (CGH) and Array-Based
CGH Technology
Chromosomal Abnormalities
Numerical Chromosomal Abnormalities
Structural Chromosomal Abnormalities
References
Exercise Questions
Additional Exercise Questions
5 Exploring DNA, RNA, and Protein Sequence Databases and
Genome Browsers
Background
General Biological Databases
RNA-Specific Databases
Protein-Specific Databases
Regulatory DNA Database
Genome Browsers
References
Exercise Questions
Additional Exercise Questions
6 Exploring Online Bioinformatics Tools
Background
BLAST
ExPASy
Clustal Omega
Reactome
References
Exercise Questions
Additional Exercise Questions
7 Multifactorial Inheritance and Common Complex Diseases
Background
Polygenic Complex Diseases
Investigating Complex Traits
Obesity as a Complex Disease
Diabetes Mellitus Type 2 as a Complex Disease
Coronary Artery Diseases as Complex Diseases
References
Exercise Questions
Additional Exercise Questions
8 Neurogenetics and Behavioral Genetics
Background
Genetic Regulation of Neural Development
Structure and Function of the Nervous System
Understanding the Genetics of Neurological Disease
Examples of Neurogenetic Disorders
Behavioral Genetics
Genetics of Depression
Genetics of Drug Addiction
Genetics of Schizophrenia
References
Exercise Questions
Additional Exercise Questions
9 Cancer Genetics
Background
Cell Cycle and Its Regulation
Oncogenes and Tumor Suppressor Genes
Carcinogens/Environmental Factors in Cancer
Breast Cancer
Role of Molecular Medicine in Breast Cancer Treatment
Recent Advances in Cancer Diagnosis and Treatment
References
Exercise Questions
Additional Exercise Questions
10 Genetic Counseling
Background
References
Exercise Questions
Additional Exercise Questions
11 Evolving Tools in Genome Editing: CRISPR-Cas
Background
Mechanism of CRISPR-Cas9 System
Applications of CRISPR-Cas9 System
References
Acknowledgment
Exercise Questions
Glossary
Index
End User License Agreement
List of Tables
Chapter 1
Table 1.1 List of selected databases accessible through NCBI’s
homepage.
Chapter 2
Table 2.1 Descriptions of the basics concepts in human
genetics.
Table 2.2 List of Mendelian traits and their associated
phenotypes and genotyp…
Table 2.3 List of Mendelian traits and their associated
phenotypes and genotyp…
Chapter 3
Table 3.1 Criteria for autosomal recessive inheritance.
Table 3.2 Criteria for autosomal dominant inheritance.
Table 3.3 Criteria for X-linked recessive inheritance.
Table 3.4 Criteria for X-linked dominant inheritance.
Table 3.5 Criteria for Y-linked inheritance.
Chapter 4
Table 4.1 Methods of chromosome banding.
Table 4.2 Name and description of numerical chromosomal
abnormalities annotated …
Table 4.3 Examples of mixoploidy.
Table 4.4 Name and description of structural chromosomal
abnormalities.
Table 4.5 Terminology and definitions of certain
chromosomal structures and so…
Table 4.6 Syndromes and associated karyotypes.
Chapter 7
Table 7.1 Some genes identified to be associated with BMI
based on genome wide a…
Table 7.2 Some genetic variations identified to be associated
with CAD based on …
Chapter 9
Table 9.1 Some oncogenes associated with certain cancers.
Table 9.2 Some tumor suppressor genes associated with
certain cancers.
Table 9.3 List of some of the identified carcinogens.
List of Illustrations
Chapter 1
Figure 1.1 NCBI Homepage (Image on Internet; accessed 12
November 2018).
Figure 1.2 NCBI homepage (All Databases; accessed 12
November 2018).
Figure 1.3 NCBI homepage (PubMed; accessed 12 November
2018).
Figure 1.4 NCBI-PubMed database searching the BRCA1 gene
(Image on internet;…
Figure 1.5 NCBI-gene database searching for BRCA1 gene
(Image on Internet; a…
Figure 1.6 NCBI-gene database searching for BRCA2 gene
(Image on Internet; a…
Figure 1.7 NCBI-gene database searching for BRCA2 gene
mouse homolog (Image …
Figure 1.8 NCBI-OMIM database homepage (Image on
Internet; accessed 11 Augus…
Figure 1.9 NCBI-OMIM database searching for muscular
dystrophy (Image on Int…
Chapter 2
Figure 2.1 Seven different morphological traits studied by
Mendel: seed shap…
Figure 2.2 Crosses between (a) two pure-breeding parental
lines and (b) hybr…
Figure 2.3 (a) Cross between parental lines, pure-breeding,
homozygous for r…
Figure 2.4 Phenotypic expressions of five different traits that
demonstrate …
Chapter 3
Figure 3.1 Basic pedigree diagram.
Figure 3.2 Tay–Sachs disease pedigree example. In this
pedigree, the disease…
Figure 3.3 Phenylketonuria pedigree example. Parental
consanguinity (shown b…
Figure 3.4 Cystic fibrosis pedigree example. The
grandparents (I-1, I-2) are…
Figure 3.5 Huntington’s disease pedigree example. This
pedigree shows that t…
Figure 3.6 Marfan syndrome pedigree example, showing that
the trait is expre…
Figure 3.7 Duchenne muscular dystrophy pedigree example.
Individual III-2 is…
Figure 3.8 Hemophilia A disorder pedigree example. If a son
(II-5) inherits …
Figure 3.9 Retinitis pigmentosa pedigree example. Children
of an affected wo…
Figure 3.10 Fragile X syndrome pedigree example. There is
no transmission fr…
Figure 3.11 Y chromosome infertility pedigree example. Only
males are affect…
Figure 3.12 Leigh syndrome pedigree example. Both males
and females are affe…
Chapter 4 Human Genetics and Genomics A Practical Guide PDF
Figure 4.1 DNA packed into chromosomes. Tightly wound,
highly repetitive het…
Figure 4.2 Centromere position distinguishes chromosomes.
Metacentric chromo…
Chapter 5
Figure 5.1 Entrez homepage (Image on Internet;
https://www.ncbi.nlm.nih.gov/…
Figure 5.2 (a) GenBank homepage
(https://www.ncbi.nlm.nih.gov/genbank/). (b)…
Figure 5.3 Rfam homepage (Image on Internet;
https://rfam.xfam.org, accessed…
Figure 5.4 Sample Rfam output (Image on Internet;
https://rfam.xfam.org/sear…
Figure 5.5 miRBase homepage (Image on Internet;
http://www.mirbase.org/index…
Figure 5.6 Results table for list of miRNAs identified in
human chromosome 2…
Figure 5.7 PDB homepage (Image on Internet;
https://www.rcsb.org, accessed 2…
Figure 5.8 (a) SMART homepage (http://smart.emblheidelberg.
de). (b) SMART d…
Figure 5.9 ENCODE homepage (Image on Internet;
https://www.encodeproject.org…
Figure 5.10 UCSC genome browser homepage (Image on
Internet; https://genome….
Figure 5.11 (a) UCSC table browser
(https://genome.ucsc.edu/cgi-bin/hgTables…
Figure 5.12 Ensemble homepage (Image on Internet;
http://www.ensembl.org/ind…
Chapter 6
Figure 6.1 BLASTN search result for an unknown DNA
sequence presented as an …
Figure 6.2 BLASTN results for an unknown DNA sequence
presented in the descr…
Figure 6.3 Six reading frame results of mAchR DNA sequence
translated with E…
Figure 6.4 Clustal Omega search page (Image on Internet;
https://www.ebi.ac….
Figure 6.5 Alignment of two human zinc finger proteins by
ClustalW. Single l…
Figure 6.6 Jalview display of an alignment of three
glucokinase DNA sequence…
Figure 6.7 (a) The steps performed to create a phylogenetic
tree using the m…
Figure 6.8 Reactome Homepage (Image on Internet;
https://reactome.org access…
Chapter 8
Figure 8.1 A schematic representation of a neuron.
Figure 8.2 A schematic representation of a synapse showing
the terminal butt…
Figure 8.3 A schematic representation of how the genetic
variations, which a…
Chapter 9
Figure 9.1 Phases and the checkpoints of the cell cycle. Green
vertical arro…
Figure 9.2 Molecular regulation of the G1 checkpoint by CDK
and cyclin prote…
Figure 9.3 (a) Mutations of proto-oncogenes to oncogenes
lead to uncontrolla…
Figure 9.4 Mutations in the BRCA genes increase the risk of
breast cancer. A…
Chapter 10
Figure 10.1 Family history of Mary.
Chapter 11
Figure 11.1 Mechanism of CRISPR-Cas adaptive immune
system. The three stag…
Human Genetics and Genomics A Practical Guide PDF Ebook

Bahar Taneri is a Professor of Molecular Biology and Genetics at Eastern Mediterranean University (EMU), Famagusta, Cyprus. After obtaining her Ph.D. degree in Biomedical Sciences, from The Rockefeller University, New York, USA in 2005, she has taught several Genetics and Genomics modules at EMU, where she has founded the Molecular Biology and Genetics undergraduate program. At EMU, she has served as the editor-in-chief of the University Research Newsletter for two years. She has also been chairing the Department of Biological Sciences since 2013. She is an affiliated Researcher of Institute for Public Health Genomics, Department of Genetics and Cell Biology, Faculty of Health, Medicine & Life Sciences at Maastricht University, Netherlands since 2011. She authored several publications in the field of genome biology and personalized medicine; and received several awards including a Fulbright Scholarship. Currently, her main research interests include human genomics, epigenomics and efficient translation of personalized genome-based findings into healthcare and medicine for prediction and prevention of common complex diseases. She is a founding member of the Medical Biotechnology Master’s program at EMU, where she teaches modules including Genome Editing.

Esra Asilmaz is currently a Locum Consultant in Gastroenterology and General Internal Medicine at Homerton University Hospital in London, UK. She obtained her Ph.D. degree in Molecular Genetics from The Rockefeller University, NYC, USA in 2004. She subsequently obtained her Bachelor of Medicine, Bachelor of Surgery degree in 2009 from St. George’s University of London, UK. Between 2009-2011, she completed an Academic Foundation Programme at St. Thomas’ and Guy’s Hospital, London, UK. During this time, she worked at Professor Trembath’s Laboratory of Human Genetics and was involved in the identification of Notch2 mutations in Hadju-Cheney Syndrome, a rare genetic condition. She was an Academic Clinical Fellow at University College Hospital, London, UK between 2011-2014 and was a member of Dr. Oben’s laboratory at The Institute of Liver and Digestive Health. She obtained her MRCP (UK) Diploma in 2014 and Specialist Examination in Gastroenterology in 2016. She obtained her CCT in Gastroenterology and General Internal Medicine in September 2019.

Turem Delikurt is a registered genetic counsellor. She graduated with a BSc in Biology from the University of South Dakota, USA in 2003. She completed her MSc in Genetic Counselling with a merit from the University of Manchester, UK in 2006. She has been working as a genetic counsellor in Cyprus since 2006. In 2015, she was registered by the European Board of Medical Genetics. Her main research interest is the exploration of genetic counselling in the context of culture. She is currently pursuing her Ph.D. degree, which is sponsored through the University of Plymouth, UK titled “Genetic Counselling in the Turkish Cypriot community”. She is dedicated to increasing awareness about genetic conditions and genetic counselling, within her community. She penned a weekly column titled “Genetics Today” at one of the main newspapers in North Cyprus from 20004 until 2017. Over the years, she has been continuosly involved in various civil society activities aimed at increasing the quality of care and life of patients and families at risk of or affected by genetic conditions in Cyprus.

Pembe Savas obtained her undergraduate degree in Medical Biochemistry from University of Leicester, UK in 2011 and further received an MSc degree in Reproductive Science and Women?s Health at University College London, UK in 2012. She has completed her project on pre-implantation genetic diagnosis of beta-thalassaemia at Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus, in 2012, where she gained hands-on laboratory experience. Since 2013, Pembe Savas is working as a senior instructor at the Department of Biological Sciences, Eastern Mediterranean University, Famagusta, Cyprus, where she is responsible for teaching numerous modules for the Molecular Biology and Genetics program; including Human Genetics. Her research interests include genetic testing in common complex diseases. Furthermore, since 2017 she has been actively involved in the Cyprus Women’s Health Research Initiative.

Seniye Targen obtained her undergraduate degree in Human Genetics from Newcastle University, UK, in 2009 and further specialized in the field of Human Molecular Genetics at Imperial College London, United Kingdom, in 2010, where she completed a project on X-linked cataract and Nance-Horan Syndrome. Upon completing her graduate degree, she has gained experience in private medical diagnostic laboratories. She had been employed as a laboratory instructor in the Department of Biological Sciences at the Eastern Mediterranean University, Famagusta, Cyprus, from 2013 to 2015. Currently, she is working towards a Ph.D. degree in molecular biology and genetics department with a particular focus on breast cancer biology at Bilkent University, Ankara, Turkey.

Yagmur Esemen is currently working as a Foundation Year Two Doctor at Charing Cross Hospital, London, UK. In 2013, she completed her undergraduate degree in Neuroscience and Biology with honors at Lawrence University, WI, USA. As an undergraduate, she has been involved in various research projects in the fields of neuroscience, molecular biology and genetics. In 2011, she spent a summer at Mayo Clinics, Rochester, MN, USA studying the effects of Bro1 family members on Vps4 activity. Her senior thesis, completed in 2013, was on investigating the neural targets of DAF-19 in C. elegans, which was awarded Summa Cum Laude honours. She has received several awards including the Howard and Helen Russell Award for Excellence in Biological Sciences. Between 2013-2014, she worked as a laboratory instructor at the Department of Biological Sciences, Eastern Mediterranean University, Famagusta, Cyprus. She obtained her Bachelor of Medicine, Bachelor of Surgery degree with distinction from St. George’s University of London, UK in 2018. Since then, she has been working as a foundation doctor in the North West Thames Foundation School in UK.