2024 A Human Genome Lecture Notes PDF

THE HUMAN GENOME Block: Foundations Block Director: James Proffitt, PhD Session Date: Monday, August 05, 2024 Time: 9:00 - 10:00 am Instructor: Casey Romanoski PhD Department: Cellular & Molecular Medicine Email: cromanoski@arizo...

THE HUMAN GENOME Block: Foundations Block Director: James Proffitt, PhD Session Date: Monday, August 05, 2024 Time: 9:00 - 10:00 am Instructor: Casey Romanoski PhD Department: Cellular & Molecular Medicine Email: [email protected] INSTRUCTIONAL METHODS Primary Method: IM07: Discussion, Large Group (>12) ☐ Flipped Session ☐ Clinical Correlation Resource Types: RE18: Written or Visual Media (or Digital Equivalent) INSTRUCTIONS/READINGS Required: Read the LEARNING OBJECTIVES and NOTES prior to attending the session. Recommended: Visit https://www.genome.gov/ to access a variety of very useful information on medical genetics and genomics that supplements what will be presented in the Foundations Block and the genetics in other parts of the curriculum. LEARNING OBJECTIVES 1. Explain the following terms: genome; gene; exon; intron; non-coding RNA; epigenetics; penetrance; variable expressivity; circulating cell-free DNA; chromatin; histone; allele; monogenic disorder; complex multifactorial disorder. 2. Describe the structures and functions of the following components of the human genome: (1) gene-coding sequences (protein-coding & non-coding); (2) gene-related sequences (introns & UTRs); (3) transcriptional regulatory elements; (4) intergenic repetitive DNA sequences (retroposons, DNA transposons, simple repeats; large repeats); mitochondrial genome; cell-free circulating DNA. 3. Outline the pathway by which nucleosomes assemble into chromatin. 4. Explain how the different the types of DNA sequence analysis and microarray genotyping are applied in the clinic. 5. Discuss the variation in genome sequences between humans. 6. Outline a strategy for counseling patients with a strong family history of breast cancer. CURRICULAR CONNECTIONS Below are the competencies, educational program objectives (EPOs), course objectives, session learning objectives, disciplines and threads that most accurately describe the connection of this session to the curriculum. Related Related Competency\EPO Disciplines Threads COs LOs CO-01 LO-01 MK-01: Core of basic sciences Genetics H & I: Medical Genetics CO-01 LO-02 MK-01: Core of basic sciences Genetics H & I: Medical Genetics Block: Foundations | ROMANOSKI [1 of 14] THE HUMAN GENOME Related Related Competency\EPO Disciplines Threads COs LOs CO-01 LO-03 MK-01: Core of basic sciences Genetics H & I: Medical Genetics CO-01 LO-04 MK-01: Core of basic sciences Genetics H & I: Medical Genetics CO-02 LO-05 MK-05: The altered structure Genetics H & I: Medical Genetics and function (pathology & pathophysiology) of the body/organs in disease CO-02 LO-06 MK-09: Critical thinking about Genetics H & I: Medical Genetics medical science and about the diagnosis and treatment of disease USMLE 1 STUDY CONNECTIONS FIRST AID FOR THE USMLE STEP 1 – 2023 EDITION: Chromatin structure: p. 32; Molecular Genetics: pp. 36-41: Medical Genetics: pp. 50-63; Oncogenes & Tumor Suppressor Genes: pp. 220-223. AMBOSS USMLE 1 Prep: Biochemistry – Genetics. https://next.amboss.com/us/article/_k05qT?q=breast+cancer#Z3186a2e5e91124c9021effe4 344433c7 CLINICAL CONTEXT The human genome is the molecular set of instructions for the structure, development, and maintenance of the body. Genomic variations can be associated with human disease. Genome-wide association studies (GWAS) have identified thousands of sequence variants that are associated with human disease. Monogenic human diseases are associated with mutations in single genes. Complex multifactorial diseases are associated with variants of multiple genes and influenced by environmental, developmental, and social determinants. Familial breast cancer is a prime example of a complex multifactorial genetic disease. In this presentation, we will look at the structure and organization of the entire set of DNA molecules within the body, which includes the nuclear genome, the mitochondrial genome, the microbiome, and the circulating genome. Using a clinical case study of a woman with strong family history of breast cancer who is worried that she may carry an inherited breast cancer- associated gene, we will show how genomics (the study of the genome) is used in the clinic to assess inherited disease risks. LECTURE NOTES Contents I. Clinical Case Presentation II. The Nuclear Genome A. Chromosomes B. Chromatin C. The Components of the Nuclear Genome i. Protein-Encoding Genes ii. Non-Coding RNA Genes Block: Foundations | ROMANOSKI [2 of 14] THE HUMAN GENOME iii. Intergenic DNA Regulatory Elements iv. Repetitive DNA Elements III. The Mitochondrial Genome IV. The Microbiome V. The Circulating Genome: Cell-Free Circulating DNA VI. Genomics in the Clinic A. Genome Variation B. Sequence Analysis C. GWAS VII. Clinical Case Discussion I. Clinical Case: A Woman Who is Concerned About Familial Breast Cancer A 32-year-old woman with two children (gravida (G) = 3; para (P) = 2; abortus (A) = 1) comes to the Ob-Gyn clinic. Her mother and maternal aunt were diagnosed with breast cancer at the age of 39 and 48 years of age, respectively. The patient is concerned that she might be at risk for familial breast cancer. A few months prior to the appointment, she had purchased a direct-to-consumer (DTC) commercial gene testing kit, which she believes measures the clinically meaningful risk of a variety of common heritable diseases including familial breast cancer. The test came back negative for breast cancer, but she is worried that the DTC test may not be accurate. As her primary care physician, she seeks your advice. II. The Nuclear Genome A. Chromosomes The haploid human nuclear genome contains about 3.2 billion base pairs (Mb) distributed on 23 chromosomes. Normally, most somatic cells in the body are diploid, with 22 pairs of the autosomal chromosomes and one set of sex chromosomes (either two X chromosomes in females or one X and one Y in males). Spermatozoa and oocytes are haploid and contain only one set of 23 chromosomes – 22 autosomes and one sex chromosome. The number of chromosomes per cell can vary in certain tissues due to genetic syndromes and in cancer cells, where aberrant chromosome duplication leads to abnormal chromosome numbers. Aneuploidy is the presence of an abnormal number of chromosomes in a cell, for example a human cell having 45 or 47 chromosomes instead of the usual 46. If a cell contains multiple complete sets of chromosomes, the cell is said to be polyploid. Karyotyping is used to assess a patient’s genome for chromosomal abnormalities associated with human diseases. During karyotyping, cells are trapped into metaphase by the drug colchicine and dropped onto a glass microscope slide, causing the cells to break open and liberate the chromosomes; this processed is referred to as a chromosomal spread. Each metaphase chromosome contains two copies of a single linear double-stranded DNA, ranging from 50 Mb on the smallest chromosome, Y chromosome, to 280 Mb on the largest chromosome, Chromosome 1. Block: Foundations | ROMANOSKI [3 of 14] THE HUMAN GENOME Chromosomes are stained with the dye Giemsa, which binds tightly to the chromatin and reveals a unique pattern of light and dark bands for each chromosome. Each band is comprised of hundreds to thousands of base pairs of genomic DNA. Each metaphase chromosome contains a centromere, which is the location where the kinetochore forms to attach it to the spindle apparatus during cell division. Each arm of the chromosome extending from the centromere is labeled as “p” for the smaller (petite) arm or “q” for the larger arm. In some chromosomes, the arms are of similar lengths, in which case the chromosome is said to be metacentric. Chromosomes in which the centromere is closer to one end than the other are termed submetacentric. In a few chromosomes, the centromere is located very close to one of the ends of the chromosome and these are termed acrocentric. A computer algorithm identifies each chromosome and assembles the chromosomes into pairs based on their sizes, centromere positions and banding patterns. Computer algorithms can also identify large aberrations in size and translocations larger than 5 Mbp. Telomeres cap the ends of each chromosome, protecting the ends from degradation and loss of genome sequences during DNA replication. The DNA sequences of the telomeres are added by the enzyme telomerase, which consists of both RNA and protein. Figure 1. The 46 chromosomes of the diploid human genome. Source: BioRender B. Chromatin The human genome contains about two meters of DNA, while the average cell nucleus is only about 20 μm. Nuclear genomic DNA in each chromosome is compacted up to 10,000-fold into a structure called chromatin by a series of protein-medicated condensation steps. In the first step of assembly 146 bp of DNA wraps approximately 2 times around a complex of two copies each of the highly basic histones H2A, H2B, H3 and H4. This DNA-histone complex is referred to as the nucleosome core particle. A variable spacer region of approximately 40-60 bp, termed linker DNA, is located in between each nucleosome core particle. The linker histones, H1 or H5 bind to linker DNA and bring the nucleosome core particles up against each other to create a chromatin filament with a width 10 nm. Block: Foundations | ROMANOSKI [4 of 14] THE HUMAN GENOME Figure 2. The nucleosome is the fundamental unit of chromatin. Source: Motifolio Many non-histone chromosomal proteins promote further condensation of nucleosomes into a coiled 30-nm structure. which is further compacted by a family of proteins known as the condensins into a 300-nm structure – the level of compaction during interphase, where most cells spend most of their existence. During the metaphase stage of mitosis, chromosomes become even more tightly condensed into the familiar looking sausage-like structures seen in karyotype maps. Figure 3. The condensation of DNA into chromosomes. Source: Motifolio C. The Components of the Nuclear Genome Protein-Encoding Genes The term “gene” refers to a segment of DNA within the genome that encodes a functional RNA – either a messenger RNA (mRNA) or a non- coding RNA. There are approximately 19,969 protein coding genes and 43,525 non-protein coding genes in the human genome. The proteins coding genes. encode messenger RNAs that are translated to produce one or more different versions of a protein. The non-coding genes encode non-coding RNAs (ncRNA) that are essential for normal cellular function and function in gene regulation, protein synthesis, RNA processing, and many other cellular processes. Non-coding RNA Genes Block: Foundations | ROMANOSKI [5 of 14] THE HUMAN GENOME Since the sequencing of the human genome, the number of genes that have been discovered to encode RNAs other than mRNAs has grown to twice the number of protein coding genes. These include genes that encode transfer RNAs (tRNA), ribosomal RNA (rRNA), small nuclear RNAs (snRNA), and microRNAa (miRNA). However, a growing number of long noncoding RNAs have been discovered that play various roles in cellular processes. Figure 4. Noncoding RNAs that Fulfill Essential Cellular Processes. Source: Takahashi et al. (2014) Hepatology 60: 744. Intergenic Sequences Sequences located in between genes are known as “intergenic sequences.” The density of genes varies within the nuclear genome with some genes located close to each other and others very far apart. The average density is one gene per 11-15 millions of base pairs. Intergenic sequences contain regulatory elements, termed enhancers, and silencers, which control the initiation of transcription from afar – anywhere from hundreds of base pairs to hundreds of thousands base pair away. Enhancers bind proteins termed transcription factors. Through DNA looping, enhancers deliver transcription factors to gene promoters to increase transcription. Silencers bind repressor proteins that inhibit transcription. Repetitive DNA Sequence Elements Greater than 50% of the human genome is comprised of repetitive DNA. Repetitive DNA ranges in size from repeated sequences of a few base pairs to thousands of base pairs. The two most common simple DNA repeats in the human genome are minisatellites and microsatellites. Minisatellite DNAs are comprised of repeated sequences of 5 to 25 base pairs in clusters of up to 20,000 base pairs. The most common type of minisatellite DNA is telomeric DNA found at the ends of chromosomes. Telomeres protect the chromosomes from being shortened during DNA replication. The sequences are added by an enzyme called telomerase, which is only present in significant quantities in rapidly dividing cells such as embryonic cells, white blood cell precursors, and cancer cells. Block: Foundations | ROMANOSKI [6 of 14] THE HUMAN GENOME Microsatellite DNA sequences are 2-13 base pair repeats that are repeated hundreds of times in clusters of up to 150 base pairs. Each person has a unique profile of different lengths of these microsatellite sequence repeats. Because of the way that they replicate during early development, expanding or contracting in size, even blood cells and gametes of identical twins are unique. Thus, microsatellites have become a tool in forensic science for detecting maternity and paternity and for identifying victims and suspects at a crime scene. Transposable Elements (Transposons): Transposable elements (transposons) are DNA sequence elements that can move to different positions within the genome. There are two classes of transposons: retrotransposons (a.k.a. retroposons) and DNA transposons. Most transposons have lost their ability to move through mutations in critical sequences required for transposition and are merely “molecular fossils of evolution. Retrotransposons move from one location to another via an RNA intermediate. The name retrotransposon comes from the fact that these DNA elements originate from RNAs that are reverse- or retro-transcribed into a complementary copy of DNA (cDNA) – the reverse process of normal transcription where DNA is transcribed to make RNA. Retroposons can be divided into two subclasses: Retroposons with LTRs are DNA sequences derived from human RNA retroviruses, which during evolution, infected humans, often with no clinical signs or symptoms. When “human endogenous retroviruses (HERVs) infected primordial germ cells (spermatogonia and oogonia) and integrated into the genome, they were passed to daughter cells, and ultimately became permanent residents of the human genome. Most LTR retroposons have lost their ability to move. The reverse transcriptase enzyme gene necessary for replication and movement became mutated and inactivated. Thus, the LTRs found at the ends of the dormant retroposons in the genome are remnants of past transposition activity and a signature of genome evolution. Non-LTR retrotransposons are not derived from viruses. These include sequences known as LINES and SINES that were originally retrotranscribed into DNA from highly abundant normal cellular RNAs. The LINE 1 reverse transcriptase functions in an analogous manner to retroviral reverse transcriptase. There are hundreds of thousands of copies of LINES per cell, and some contain genes for ncRNAs. LINE 1 sequences are the only LINES still active in retrotransposition. The LINE-encoded ncRNAs bind and repress retrotransposition of LINE 1 sequences to safeguard the genome. Several cancers including some leukemias occur when LINE 1 is retrotransposed into important cellular genes, disrupting their function – a process known as insertional mutagenesis. SINES are non-LTR retroposons that are even more abundant than LINES. Alu SINE sequences are present in more than a million copies per genome. SINES do not contain a gene for their own reverse transcriptase and borrow the LINE 1 reverse transcriptase to move around the genome. DNA transposons move by using their own encoded transposase enzyme via a “copy-paste” mechanism. During human evolution, DNA transposon simply change location, but do not increase in copy number. DNA transposons comprise about 3% of the genome but have lost their ability to move due to mutations in their transposase and are considered “molecular fossils.” However, Block: Foundations | ROMANOSKI [7 of 14] THE HUMAN GENOME they DNA transposons provide very useful landmarks in analyzing whole genome sequences. Figure 5. The Classes of Repetitive DNA in the Human Genome. Source: BioRender III. The Mitochondrial Genome Mitochondria, the organelles where most of the cellular energy is produced, contain a circular DNA genome of about 16,000 base pairs or 16 kilobase pairs (Kb) long. The average large somatic cell like a liver cell or a cardiac muscle cell contains 1000-10,000 mitochondria while a skin cell may contain only a few hundred. A sperm cell contains only 50-75 mitochondria, almost exclusively to provide energy for the motion of the sperm tail. Mitochondria usually contain a single copy of circular double-stranded DNA genome with 37 genes and no introns. Most of those genes encode tRNAs for the translation that the mitochondria use to carry out with their own ribosomes. Only 13 mitochondrial genes encode proteins, but mitochondria contain hundreds of different proteins. Most mitochondrial proteins are encoded by genes in the nuclear chromosomes and are translated in the cytoplasm and then imported into the mitochondria. When a sperm enters the cytoplasm of the egg during fertilization, the sperm mitochondria are destroyed; thus, mitochondrial DNA is maternally inherited. Maternally inherited mitochondrial DNA is used to trace human evolution. Figure 6. The mitochondrial genome. The 16.6 kbp genome contains 37 genes that encode only a small fraction of the proteins and RNAs in the mitochondria – the nuclear genome encodes most mitochondrial proteins and RNAs, which are subsequently imported into the mitochondria. Source: Wikipedia Figure 7. The mitochondria in the sperm cell are located just below the base of Block: Foundations | ROMANOSKI [8 of 14] the sperm head, which contains the nucleus and most of the cytoplasm. The mitochondria are destroyed upon entrance into the egg during fertilization. Source: A-Level Biology THE HUMAN GENOME IV. The Microbiome The human body contains the DNA of microorganisms that inhabit the human body – bacteria, fungi, and protozoa, referred to as the microbiome. The number of cells in the microbiome is estimated to be about two times the number of human cells. The weight of the human microbiome is approximately 2-5 pounds for an average adult. Each part of the body has a unique microbial composition. The nasal and oral cavities, the skin and GI tract each have unique microbial populations, and each region of these organ systems has a distinct microbial species profile. No two humans have the same microbiome. The microbiome consists of the over 1,000 different bacterial and fungal species. But their genomes are not completely isolated from the human cellular genome. These microbes can pick up small pieces of DNA from broken human cells and incorporate these sequences into their own genomes. The microbiome plays essential roles in human health and disease. Many essential metabolites are synthesized by the gut microbiome, including certain bile acids, short- chain fatty acids, and branched chain amino acids. Trimethylamine N-oxide and other compounds produced by the gut microbiome have been strongly implicated in the pathogenesis of specific metabolic diseases. The optimal balance of microbial species is essential for human health, and disruption of the microbiome due to drugs (e.g., antibiotics) and improper diet is associated with numerous disorders. Figure 8. The human microbiome is dispersed through the interior and exterior of the body. Source: National Institutes of Health V. The Circulating Genome Circulating cell-free DNA (ccf-DNA) refers to fragments of DNA from tissues and organs that are released into the circulating blood and lymphatic systems. In addition, ccf- DNA from fetal and tumor cells can also be found in circulating fluids. symptoms. Biomarkers are also useful in monitoring the effects of therapeutic interventions where monitoring of the disease is impossible or impractical. ccf-DNAs are currently under intense investigation for their value as diagnostic biomarkers to allow a Block: Foundations | ROMANOSKI [9 of 14] THE HUMAN GENOME physician to detect a disease prior to clinical presentation of signs and for example, the effects of a drug that might forestall the appearance of an adult-onset cancer might be monitored by looking for cf-DNA that was shed by tumors too small to be detected by imaging. cf-DNA can also be used to monitor tumor metastases and disease recurrence after surgery. Figure 9. The circulating genome is comprised of DNA from healthy somatic cells, tumor cells, the microbiome, and in the case of pregnancy, fetal DNA. Source: Wikipedia VI. Genomics in the Clinic: Genome Variation, Sequencing, and Disease Association Genome Variation The variation in nuclear genome between any two individuals is estimated to range from 0.1% to 0.6%, depending on the populations being compared. No two human beings have the exact same genomes. Even monozygotic twins, who originated from the same fertilized oocyte, accumulate genomic DNA sequence variants very early in embryonic development. Differences in nucleotide sequence within or among populations are referred to as genetic polymorphisms and arise through the process of mutation. It is estimated that each person has 50-100 new sequence variants compared to the parents. A sequence variant of a specific gene is referred to as an allele. Depending on the sequence variations, different alleles may or may not affect the function of the gene product (i.e., protein or ncRNA). Molecular Techniques to Detect Alterations in the Genome Have Ushered in a New Era of “Precision Medicine.” Most genomic alterations associated with human diseases are including point mutations, small deletions, and insertions (INDELS) and expansions are much smaller in size than can be detected by light microscopy. Various molecular techniques have been developed to detect changes in the genome at the resolution of a single base pair. The methods for genome analysis are discussed below. Genome Sequence Analysis The original DNA sequencing methods used to sequence the human genome relied on a method referred to as chain termination sequencing or Sanger Block: Foundations | ROMANOSKI [10 of 14] THE HUMAN GENOME sequencing, named for the inventor of the technology, Fred Sanger. This method was based on sequencing a few hundred base pairs at a time and assembling the sequences by computer. However, Sanger sequencing, even when fully automated, is not rapid enough to sequence a whole genome on the time scale to be useful in clinical diagnostics. New technologies, termed next generation (NEXGEN) sequencing, quickly evolved to permit extremely rapid sequencing of whole genomes. In NEXGEN sequencing, very short fragments (10-20 bp) are read and then assembled into complete genome using reference genomes. NEXGEN sequencing allows for a complete genome to be obtained in about a day. NEXGEN genome sequencing methods rely on reference genomes for assembly of the genome. The overall human genomic variation of less than 0.1 to 0.6% appears to be valid regardless of race, ethnicity, or population, but members within these groups will generally have a greater number of common genomic variants than individuals outside the group. Thus, when using reference genomes for whole genomic analysis, it is essential to use a reference genome that is derived from the appropriate population. However, the short reads in NEXGEN sequencing can result in multiple errors, which in a clinical setting may have important consequences. Long-read DNA sequencing methods and bioinformatics have revolutionized genomic analysis. Although the human genome was declared “complete” in 2003, 8% of the genome with highly repetitive DNA (e.g., centromeres and telomeres) was refractory to short-read sequencing methods. In 2022, the entire genome was completed using advances in bioinformatics and newly developed long-read DNA sequencing methods. The most common long-read sequencing method involves laser detection to read a DNA sequence as it is extruded through a nanopore are enabling the sequencing of very long fragments of genomic DNA, on the order of several thousand base pairs in a single read. As the accuracy and speed of long-read sequencing improve, it will become routine in clinical medicine and a patient’s genome become part of their electronic medical record (EMR). Microarray Genotyping Microarray genotyping is a very fast and inexpensive method for detecting single nucleotide variants (SNVs), also referred to as single nucleotide polymorphisms (SNPs). This highly automated technique is based on microarrays of short DNA fragments attached to silicon or glass surfaces. Tens of thousands of spots containing short DNA fragments representing all the protein encoding genes within the human genome are printed onto the microarray substrate surface in pattern that allows for automated identification of each spot in the array. Patient and reference DNAs are fragmented and labeled with fluorescent dyes. The patient DNA fragments are applied to the microarrays, and if they share a sequence with the DNA in the spot, they will “anneal” or “hybridize” to the spot providing a fluorescent signal that can be observed by a fluorescence detector. Microarray genotyping is the primary method used by direct-to-consumer (DTC) DNA testing companies such as 23andMe and Ancestry.com. However, microarrays can be designed for specific diseases that are used by clinical laboratories for rapid genetic disease diagnosis as well as to detect mutations in tumor samples. Targeted and Gene Panel Sequencing Predesigned gene panels contain only important genes or gene regions associated with a specific disease or phenotype, selected by expert guidance. By focusing only on the genes most likely to be involved, these panels conserve resources and minimize data Block: Foundations | ROMANOSKI [11 of 14]  THE HUMAN GENOME analysis considerations. Predesigned gene panels are readily available from commercial sources for many different genetic disorders. Whole Exome and Whole Genome Sequencing (WES & WGS) WGS is the gold standard for detection of disease-associated gene variants. While WGS is very useful when there is not enough information from other diagnostic tests to point to a cause for a genetic abnormality, the large amount of information provided by WGS can be overwhelming. Thus, a physician may elect to order a WES analysis. In WES, the mRNA from the patient is isolated and reverse transcribed into complementary DNA or cDNA, and the cDNA is then sequenced by high throughput DNA sequencing. Thus, WES only reveals the regions of the genome that are transcribed and then translated to make proteins. But only 50% of all disease-associated mutations are found in the protein-coding regions, with the rest found in introns and in the intergenic regions. With the time required for analysis of WGS results constantly improving, WES may soon become obsolete. Genome-Wide Association Studies A genome-wide association study (GWAS) is an approach to identifying genes associated with a particular disease. GWAS involves sequencing of genomes of unaffected individuals and comparing these sequences with those of individuals with a specific disease, disorder, genetic trait. The validity of a GWAS is predicated on comparing sequences of individuals with the same ethnic and racial backgrounds. VII. Case Study Discussion: A Woman Who is Concerned About Familial Breast Cancer The following would be part of a discussion with the patient: A. Risk Factors for Breast Cancer Female & age – most breast cancers are diagnosed in women after the age of 50. Family history Inherited gene variants – most common genes are BRCA1/2, but there are many others. Reproductive history – early menstruation and late menopause are associated with longer exposure to estrogen – a tumor growth promoting hormone. Dense breast tissue Previous cancers at other sites B. Recommendations based on National Comprehensive Cancer Network (NCCN) Guidelines Explain that familial breast cancer can be due to mutations in any one or more of multiple gene sequences. Explain the difference between DTC tests and clinical tests. Based on very strong family history, order a breast cancer gene panel DNA sequencing screening test, and if necessary, order WES or WGS. Block: Foundations | ROMANOSKI [12 of 14] THE HUMAN GENOME If BRCA1/2, TP53, PTEN, PALB2, BRIP1, ATM, CHEK2 mutations are found, suggest the following: Learn to be aware of changes in breasts beginning at age 18. Clinical breast exam every 6-12 months beginning at age 25. Annual breast MRI with contrast (or mammogram if MRI is unavailable) beginning at age 25 and continuing to age 75. Screening after age 75 should be considered on an individual basis. Consider participation in an imaging or screening clinical trial. Practice Exam Questions 1. Which one of the following best describes the most common type of DNA analysis carried out by the direct-to-consumer (DTC) genetic testing service? A. Whole genome sequencing B. Whole exome sequencing C. Partial exome sequencing D. Partial genome sequencing E. Microarray SNP analysis 2. Which one of the following best characterizes the histone composition of the nucleosome core particle? A. (H2A)1, (H2B)1, (H3)1, (H4)1 B. (H2A)2, (H2B)2, (H3)1, (H4)1 C. (H2A)2, (H2B)2, (H3)2, (H4)2 D. (H2A)1, (H2B)2, (H3)2, (H4)2 E. (H2A)2, (H2B)2, (H3)2, (H4)1 3. What it the range of normal genetic variation between a female from South Dakota in North America and a female from Kenya in Africa? A. 0.1 - 0.6% B. 1% - 2% C. 2%- 5% D. 5% -10% E. 10%-20% 4. Which one of the following is characteristic of all retrotransposons? A. The presence of long terminal repeats at the ends of the transposon B. Insertion into the genome that involves an RNA source C. DNA polymerase to copy the retrotransposon into DNA for insertion into the genome D. Excision of the retrotransposon as the first step in the retrotransposition E. Retrovirus infection 5. Which one of the following would be most useful diagnostic strategy to screen a patient’s genome for cancer-related inherited mutations? A. Whole genome sequencing B. Whole exome sequencing Block: Foundations | ROMANOSKI [13 of 14] THE HUMAN GENOME C. Gene panel sequencing D. Karyotype E. Family medical history Answers: 1-E; 2-C; 3-A; 4-B; 5-A or C Block: Foundations | ROMANOSKI [14 of 14]