Diego HerreraCancer and Society

Background Advances in biotechnology have decreased the

expense of sequencing an individual’s genomic information, giving patients the option to know the likelihood of developing a disease or condition

How? The structural deviations in a person’s genetic code is

compared to the ‘human reference genome’ Depending on the region of the genome, detection of

these mutations allows clinicians to provide patients with likelihood ratios (LR)

Purpose To examine and explore the determinants, as well as,

the social implications of measuring an individuals LR Demonstrate the significance in helping to treat or cure

cancer

Personal genome sequencing Inherited genetic mutations of an individual are found by

comparing their sequenced data to a human genome without mutations that decrease fitness

Genome without mutations Created in ‘The Human Genome Project’ Referred to as the ‘human reference genome’▪ Derived from clone-based and random whole genome shotgun

sequencing strategies Two versions of reference genome

Human Genomic Sequencing Consortium▪ Composite derived from haploids of numerous donors▪ Primarily of European origin and is estimated to be aprox.

99.99% accurate with aprox. 210 gaps Celera Genomics▪ Consensus sequence derived from five individuals

Errors are also known as ‘structural variants’ Single nucleotide

polymorphisms (SNPs) Indels Deletions Novel Insertion Inversion

Compares human genomic reference sequence with individual’s diploid genome

Structural variants (SVs) due to large deletions are identified using long-sequence reading techniques (see Table below) to span missing segments Maps the adjacent, but discontinuous regions of the genome Termed ‘Phasing of Alleles’

Paired-end mapping Detects inversionsApproximately 10% of SVs >2kb in size

Split-read mapping Breakpoint identification of copy-number variants (CNVs)Typically requires 75- to 100-nt to capture most deletions

Read depth Determines the frequency of ‘reads’ in a DNA segment, which reflects its copy number

Local Reassembly Requires the use of DNA microarrays and comparative genome hybridization. The intensities of hybridization are relative to the reference sample copy number

Local reassembly Incorporates both comparative and de

novo methods Most of assembly can be done based on

the existing reference genome▪ Generally unnecessary to perform an

experimentally and computationally intensive whole-genome de novo assembly▪ May be necessary in regions with complex

SVs and for new sequences to identify different types of variant events such as undiscovered cancer genes

Steps 1 & 2 The generated reads are first

mapped to the reference genome to call high-quality SNPs and small Indels

Step 3 SVs based in aberrant

alignment formation Step 4

The novel insertions can be reconstructed using local de novo assembly algorithms

Step 5 The final phasing step will be

able to deduce the complete genome of the individual

Complete human genome sequencing is more readily available due utilization of massively parallel genomic micro- and nanoarrays Sequencing efficiency is increased by

▪ Miniaturization to incorporate more DNA spots/mm^2 on each array chip▪ Designing faster imaging cameras, brighter dyes, haplotyping and other

improvements Reduction in costs

▪ Increase in sequencing efficiencies mentioned above▪ Improvements in assay production for existing platforms▪ Development of novel technologies such as single-molecule sequencing

Number of specialized genomes sequenced is growing exponentially From <100 in 2009 to >2000 in 2010 The journal, Nature, estimates 25,000 genomes will be sequenced by the

end of 2011 $1,000 to sequence a ‘personal genome’

Predicted to be achieved in 2014 with existing DNA nanoarray technologies▪ Pioneered by Complete Genomic’s Analysis (CGA®) Platform

Expected engineering advances to drop costs significantly below this mark in following years

The graph on the left shows an inverse relationship of two factors: fiscal expense of sequencing and the number of genomes created. As the sequencing cost per base has decreased, the number of completed genomes have increased. The table on the right shows the specialized genomes that implemented recently developed high-throughput DNA sequencing techniques. This technology was not available to researchers of the Human Genome Project.

Step 1: Formation of DNA Nanoballs (DNBs) Each DNB contains hundreds of copies of the 70 bases sought to be read in each fragment

Diameter of each spot is 300 nanometers. The space between each spot is 700 nanometers. There are 2.8 billion spots in the area of the chip: 25 millimeters wide and 75 millimeters long

Step 2: PlatingFill spots with sticky DNBs. Each nanoballarray chip contains 180 billion bases of genomic DNA for imaging

Step 3: Imaging Detection of red, blue, green and yellow fluorescence. High accuracy makes it possible to read seven 5-base segments from two ends. Total of 70 bases read in each fragment

Illumina® Founded in 1998 One of the world’s leading providers of intergraded tools and

services to advance the understanding of genetics and health In 2009, was the first to generate a personal genome sequence

in a clinical laboratory setting Prior to ordering

Meet with geneticist/genetic counselor to review important considerations▪ Decide what genetic information is of interest▪ Determine which additional information may or may not want to learn

Clinical geneticist Certified by the American Board of Medical Genetics

▪ Requires 4-5 years of combined residency such as Internal Medicine/Medical Genetics or Pediatrics/Medical Genetics

Medical genetics differs from the field of human genetics in its specific application of genetics towards medical care▪ Recognized by the American Board of Medical Specialties as a primary

medical specialty

Requisition Form Doctor determines if IGS is the appropriate course of action and

is the only person that can order test Sample Collection

Blood and saliva ▪ Sequencing is performed on DNA extracted from blood sample▪ Saliva is used to verify identity of blood sample and for quality control

▪ Needs to be taken in doctors presence Analysis

Processed confidentially by validated laboratory procedures in CLIA-certified, CAP-accredited facilities

Time Frame Results returned to doctor in 90 days

Costs IGS for Preventative care genome sequencing: $9,500 IGS for Medically relevant genome sequencing: $7,500 IGS for Cancer patient sequencing: 2 for $10,000

USB storage device DNA data can only be sent to doctor through

mail on a flash drive Requires scheduling follow-up appointment to

review information Results contain multiple reports which

include Genome sequence, covering greater than

90% of the known human genome List of DNA variations compared to the human

reference genome and the dbSNP database Charts and graphs depicting how DNA

variations are distributed in genome

Current annual healthcare costs in the United States is estimated to be $2.6 trillion The cost of sequencing 26 million genomes per year

(e.g., newborns, adults, and cancer biopsies) at $1,000 per genome would represent 1% of this amount at $26 billion

Estimated reduction in healthcare costs by at least 10% or $260 billion▪ Potential savings of more than $234 billion while enabling

better, more personalized health care Personalized genomes can serve as the ‘universal

genetic test’, replacing hundreds of individual tests The majority of cystic fibrosis tests do not cover the 20%

of cases caused by less frequent mutations Currently, BRCA genes are the only tumor suppressor

genes routinely sequenced to enhance tumor prevention

TCGA is a project, started in 2005, to catalogue genetic mutations responsible for cancer, using high-throughput DNA analysis techniques Represents effort in ‘War on Cancer’

Goals Advance personalized medicine Improve ability to diagnose, treat and prevent

cancer through a better understanding of the molecular basis of a disease

Patient cohort integrated study 500 patient cancerous tissue samples will be

analyzed for each type of tumor 6,000 candidate genes and microRNA segments will

have entire genomes sequenced

Circos Plot Visualization tool

to facilitate the identification and analysis of similarities and differences arising from comparison of genomes collected so far in TCGA Project

Genomic information from TCGA has led to developments and FDA approval of recent cancer treatments

Targeted cancer therapies Drugs or other substances that block the

growth and spread of cancer by interfering with specific molecules involved in tumor growth and progression

Currently, there are 34 FDA approved targeted therapies

Non-receptor tyrosine kinase inhibitors Ex. Gleevec®

▪ Treats gastrointestinal stromal tumors by blocking tyrosine kinase enzymes Though approved by the FDA in 2001, it was further granted efficacy to

treat 10 more types of cancers in 2011 Histone deacetylase inhibitors

Ex. Zolinza® ▪ Treats cutaneous T-cell (CTC) lymphoma by inhibiting the activity of histone

deacetylases▪ Results in the removal of acetyl groups in proteins that regulate gene expression

Proteosome inhibitors Ex. Velcade®

▪ Treats mantle cell lymphoma by causing cancer cells to die through interference of proteasomes, thereby disrupting enzymatic function

Angiogensis inhibitors Ex. Avastin®

▪ Treats glioblastoma by binding vascular endothelial growth factor (VEGF) with monoclonal antibodies to prevent new blood vessel formation

Immunosuppressants Ex. Rituxan®

▪ Treats B-cell non-Hodgkin lymphoma by binding CD20, resulting in the activation of the immune system to target B-cells for destruction

Genetic Information Nondiscrimination Act (GINA) Bill passed in 2008 Prohibits the improper use of

genetic information in health insurance and employment

Health insurance▪ Prohibits group health plans and

health insurers from denying coverage to a healthy individual or charging that person higher premiums based solely on genetic predisposition

Employment▪ Bars employers from using

individual’s genetic information when making hiring, firing, job placement or promotion decisions Scene from the film, Gattaca

Film Code 46 Insurance agencies have gained

power to access peoples genetic information in order to issue or deny insurance

Insurance agencies have the authority to deny access to modern cities and economy

Issues Genetic passports

▪ Citizens not to genetic standards are deported

▪ Russian and Canadian governments are battling legislation to issue passports containing genetic information for identification and crime prevention purposes

Genetic enhancement▪ Viruses are engineered to enhance

abilities such as being able to sing in tune or to speak a foreign language

▪ Very similar to gene therapy where viruses are used as vectors to combat disease

Fictional viruses engineered to help an investigator solve a case by enhancing his emotion of empathy

Drug discovery May shorten the length of clinical trials

▪ Exclude subjects that are more likely to be non-responders and those with greater risk of side effects

Associated risks Limited knowledge

▪ Limited understanding does not mean personal genomes have no current application

▪ 3,000 genes for which interpretative information would be immediately useful Unnecessary medical actions

▪ Validated genome interpretation software using conservative reporting standards is a potential solution

▪ Physician and patient education programs need to be introduced, so that the genotypic data is understood within a broader biological and statistical context▪ Ex. Personal medical history, family history and other behavioral or molecular phenotypic

data Favorable circumstances

Unlikely that the trend of increasing medical costs in the United States will be sustainable

May motivate influential authorities in government and medicine to adopt preventative and predictive medical practices based on genetic knowledge

The Cancer Genome Atlas Project Will lead to a detailed understanding of the diverse molecular processes in

cancer development and metastasis Enable the development of improved tumor diagnosis, classification and

selection of more effective treatments Novel discoveries and inventions

Required for full integration in medical practice▪ Personal genome sequencing is being enabled by unprecedented advances in complete

genome sequencing technology▪ Medical genomics software improvments are also occurring rapidly, driven by the need to

interpret the influx of data from thousands of genome sequences Conservative control

Threats of discrimination and privacy violations must be treated seriously ▪ Education

▪ Programs must inform citizens with accurate information and have a strong presence in academia▪ Necessary in an effort to not only curb discrimination or public fervor, but to inform people of their

rights▪ Policies

▪ The Genetic Information Non-discrimination Act Prohibits discrimination on the basis of genetic information with respect to health insurance and

employment▪ The implementation of this law and other supporting non-discriminatory policies must be continued and

reinforced▪ Data reporting standards

▪ Data should be stored electronically, preferably as part of an individual’s electronic medical record▪ Only doctors can have access, but only when required

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