new gen diagnostics Flashcards
1
Q
Next generation DNA sequencing (NGS)
A
a number of different modern sequencing technologies
2
Q
Examples of next generation DNA sequencing
A
llumina (Solexa) sequencin
Roche 454 sequencing
Ion torrent: Proton / PGM seque
ncing
SOLiD sequencing
3
Q
Purpose of NGS
A
These recent technologies allow us to sequence DNA and RNA much more quickly and cheaply than the previously used Sanger sequencing, and as such have revolutionised the study of genomics and molecular biology.
4
Q
Whole exome sequencing (WES)
A
massively parallel NGS of exonic sequences
5
Q
Purpose of WES
A
WES has been enormously successful in the identification of novel Mendelian disease associated genes, and it has recently begun to be used for clinical diagnostics.
6
Q
Personalised medicine
A
detect and eliminate tumors before they become life threatening–before they are even visible on medical images, get diagnostics to the most sensitive level possible
7
Q
Next generation diagnostics functions
A
In general,
- Very predictive and allegedly accurate
- Lowers the risk of developing diseases due to being
- Able to actively seek out preventive measures
- Knowledge from the genome data collected can contribute to genome mapping and trace the history and development of pathogens
- Helps to control disease outbreak
8
Q
Next generation diagnostics
A
Next-generation sequencing and personalized medicine
9
Q
the shift of the emphasis of care
A
Prevention -> Early detection of disease -> Management of multiple chronic conditions
With current trends and time, the emphasis of care is shifting toward prevention and early detection of disease, as well as management of multiple chronic conditions. instead of focusing on finding cures. We only do so when endpoint of diseases are reached.
10
Q
Point of care (POC) diagnostics
A
Defined as tests that are carried out near site of patient care AND outside a centralized laboratory
11
Q
The 4 key requirements of POC
A
- simple to use
- reagents and consumables are almost in storage and usage
- device together with associated reagents and consumables are safe to use
- results should be concordant with an established laboratory method
concordant - in agreement with
12
Q
Goal of POC
A
minimise the time to obtain a test result, allowing clinicians and patients to make a quick clinical decision
gives immediate results in non-laboratory settings to support more patient-centered approaches to healthcare delivery.
allows patient diagnoses in the physician’s office, an ambulance, the home, the field, or in the hospital. The results of care are timely, and allow rapid treatment to the patient
13
Q
Outcomes of the goals of POC
A
Facilitate immediate evidence-based medical decisions that improves patients’ outcomes
Reduce patient acuity, criticality, morbidity and mortality especially during life-threatening crises and emergency resuscitations
14
Q
Guidelines issues for PoCT devices assured guidelines provided by WHO
Assured
A
Affordable – for those at risk of infection
Sensitive – minimal false negatives
Specific – minimal false positives
User-friendly – simple to perform, uses non-invasive specimens
Rapid & Robust – short turnaround time and no need for refrigerated storage
Equipment-free – no complex equipment
15
Q
Exceptions to assured guidelines
A
However, GUIDELINES for those developing PoCT devices for the detection of sexually transmitted infections (STI) provided by WHO may defer:
For PoCT devices that will be used in the developed world, some of the ASSURED criteria will also remain relevant but others will be substantially different. Thus instead of being equipment free, the need will be for relatively sophisticated equipment that at a minimum can provide a quantitative result, presentation of the results, decision support and, ideally, connectivity to other information systems such as the patient’s electronic health record. While the technology to provide all these features undoubtedly exists, they come at a cost which may be difficult to recover using the most common business model for PoCT which is that used for the central laboratory, based on complexity and reagent costs, thus only charging for the test strips/cartridges. When one combines these equipment needs with what are seen as other competitive requirements such as a small sample volume, whole blood, production of a result within 10 min of applying the sample, ease of use and requisite analytical performance, it is possible to appreciate the technological challenges involved in building such devices.
16
Q
PocT market
A
over-the-counter products such as glucose monitoring and pregnancy testing
and
professional market includes all other testing including critical care, infectious disease, cardiac markers, diabetes, lipids, coagulation and haemotology
17
Q
Basic dipsticks as with urinalysis
over-the-counter POC
A
a urine sample is applied to a porous pad containing reagents and a reflectance technology is used to provide a semi-quantitative estimate of the analyte
18
Q
Handheld devices like glucose meters
over-the-counter POC
A
get a drop of blood and apply the blood to the test strip when the blood symbol appears in the meter window
the meter will count down and display the result of blood glucose
19
Q
Rapid diagnostic tests
examples of POC diagnostics
A
Rapid antibody tests
- rapid HIV test
- rapid plasma reagin
Rapid antigen test
- rapid influenza diagnostic test
- malaria antigen detection test
- rapid strep test
20
Q
Spartan RX platform
to detect mutations in the CYP2C19 gene, which codes for the CYP2C19 protein in the body.
A
DNA testing
Mutations in the CYP2C19 gene cause reduced response to clopidogrel, an anti-platelet aggregation drug given to patients undergoing percutaneous coronary interventions (PCI), resulting in adverse consequences
PCIs are often performed urgently, hence the potential benefits for rapid PoCT to detect mutations in the CYP2C19 gene and alternative drug therapy with better outcomes.
The desktop instruments can extract and analyze DNA from a buccal swab. It is then placed in a cartridge and inserted into the instrument and results come out in 1 hour.
There is limited data on the outcomes of using the test but the test was useful in identifying patients at risk of a poor response to clopidrogrel.
21
Q
POC diagnostics in Singapore
A
BiosensoriX sells a variety of POC detection products for research use only
ELLI tm, Stack Pad tm, Quiz PCR Biochip Test
22
Q
ELLi tm
A
a POC test for research use only
ELLI™ is a USB-like device that enables accurate quantification of biomarkers and pathogens for a range of antibody-based assays
- target applications that requires test and accurate biomarkers measurements
- dengue triage
- stroke triage
- acute kidney injury
23
Q
Features of ELLi tm
A
- Easy multiplexing (multiple signals are combined into one signal over a shared medium)
- One step procedure
- High sensitivity
- Accessible to everyone
24
Q
Cell ID Singapore
A
Portable genetic test for Covid-19
Using a nasal swab or saliva specimen, this portable genetic test uses rapid molecular testing to determine in minutes, anywhere, anytime, if a person has COVID-19 or not
They detect the genetic information of the virus, the RNA
25
Features of Cell ID Singapore Quiz PCR BiochipTest
Nasal Swab
One step procedure
Immediate Results
Contact Trace
26
Emerging POC Diagnostics function
1. Blood Glucose Testings (effective options for frequent and timely measurements of blood glucose)
2. Cancer biomarker (simplifying cancer biomarker test)
3. HIV testing (increase the coverage of testing and expand the scope of this technology to the rural populace)
4. Portable PCR test for COVID-19 (test to be sued outside of a laboratory setting and by healthcare professionals on the pandemic front lines)
27
Future POC diagnostics
Microbiology
- outbreaks
- methicillin resistant staph. aureus
```
Endocrine testing to guide surgical therapy
Para-thyroid hormones
- ACTH (adrenocorticotropic hormone)
- Gastrin
- Growth Hormones
```
Sepsis Markers
Stroke Markers
DNA Testing
28
background of ACTH
a polypeptide tropic hormone produced and secreted by the anterior pituitary gland. It is also used as a medication and diagnostic agent
29
Why think about ACTH ?
Deficiency of ACTH is a sign of secondary adrenal insufficiency (suppressed production of ACTH due to an impairment of the pituitary gland or hypothalamus, cf. hypopituitarism) or tertiary adrenal insufficiency (disease of the hypothalamus, with a decrease in the release of corticotropin releasing hormone CRH).
Conversely, chronically elevated ACTH levels occur in primary adrenal insufficiency (e.g. Addison's disease) when adrenal gland production of cortisol is chronically deficient.
In Cushing's disease a pituitary tumor is the cause of elevated ACTH (from the anterior pituitary) and an excess of cortisol (hypercortisolism) – this constellation of signs and symptoms is known as Cushing's syndrome.
30
Future POC Diagnostics - AI Technologies
1. Detecting Diseases - AI-based software can tell if a patient has a certain disease even before evident symptom appears
2. Classifying diseases - accurately spot signs of a certain disease in medical images such as MRIs, X-rays, and CT scans
3. Improving decision making process - help doctors to overcome research obstacles, process vast amounts of health data quickly, and ensure holistic understanding of a patient health
4. AI-based treatment solutions - improve surgical robots that execute highly complex operations
5. Making people live longer - help track immunosenescence levels and identify new interventions designed to boost the immune system
31
Multiple POC testing (xPOCT)
1. the stimulatenous on-site detection of different analytics from a single specimen
2. gathered increasing importance for clinical diagnostics with emerging applications in resource-based settings
3. in addition, it is highly desirable to screen various analytes simultaneously, enabling a rapid, low-cost and reliable quantification
4. However, in many instances, clinical evidence based on a single biomarker is not sufficient for an adequate diagnosis of a disease and monitoring of a treatment
32
Multiplexed-point-of-care testing (xPOCT)
simultaneous on-site detection of different analytes from a single specimen, has recently gained increasing importance for clinical diagnostics, with emerging applications in resource-limited settings (such as in the developing world, in doctors’ offices, or directly at home).
33
clinical xPOCT applications available
many different commercial devices for the simultaneous detection of clinical chemistry parameters, including blood gases, and electrolytes, or acute metabolites such as Abbott i-STAT system, Abaxis Piccolo Xpress, or Nova Biomedical StatSensor), or immunoassays (e.g., Radiometer AQT90 Radiometer and Mitsubishi PATHFAST analyzer
These systems are either bulky and expensive bench-top bioanalyzer, or only capable of detecting a limited amount of type of analytes
34
the future of xPOCT device will be driven by
1. novel biotechnologies
2. targets (e.g circulating RNAs, or tumor cells, exosomes and miRNAs)
3. applications like personalized medicine, homecare monitoring and wearable
35
Requirements of xPOCT devices
1. easily accessible
2. user-friendly
3. rapid-turnaround times
4. longer shelf life
5. accurate and quantitative results
6. low-cost and portable devices
7. Hi-technology devices
easily accessible - low sample consumptions or possibility to use easily accessible or noninvasive to obtain a maximum amount of information from valuable specimens
user-friendly - simple or automated system operation requiring minimal user interaction
rapid turnaround times - allow an intermediate treatment
longer shelf life - prolonged reagent storage and shelf life
accurate and quantitative results - in accordance with clinical and central laboratory findings, adhering to international quality standards
low-cost and portable devices - equipped with disposable and cartridges or strips
Hi-technology - equipment-free or cell-phone-based systems are highly-preferred
36
full requirements of xPOCT diagnostic devices
(i) low sample consumption (e.g., blood from a finger prick), or the possibility to use easily accessible (noninvasive) samples, like urine, saliva, sweat and breath condensate, along with a maximum amount of information obtained from valuable specimens
(ii) simple or automated system operation requiring minimal user intervention
(iii) rapid turnaround times – within 10 minutes to 2 hours – allowing an immediate treatment
(iv) prolonged reagent storage and shelf life
(v) accurate and quantitative results in accordance with clinical and central laboratory findings, adhering to international quality standards (ISO 15189);
(vi) low-cost and portable readout devices, equipped with disposable test cartridges or strips, satisfying the in vitro diagnostics guidelines (EU Directive 98/79/EC or FDA regulations). Finally, equipment-free or cell-phone-based systems are highly preferred in the developing world or other resource-poor settings [4, 5]. Ideally, the xPOCT device should also be able to analyze different types of compounds simultaneously, e.g., RNAs, metabolites, proteins, exosomes, and cells.
37
ideal xPOCT device
should also be able to analyze different types of compounds simultaneously
38
microfluidic paper-based analytical devices - μPADs
low cost - Low-cost xPOCT solutions have attracted particular interest in the developing world, e.g., for hepatotoxicity screening.
side effects - Low-cost xPOCT solutions have attracted particular interest in the developing world, e.g., for hepatotoxicity screening.
liver function testing - On-site testing by gauging the levels of two liver enzymes in whole blood, aspartate aminotransferase and alanine aminotransferase
colorimetric readout - It offers results with both qualitative and quantitative data analysis within 15 min after the sample introduction (< 35 μl blood
39
examples of Microfluidic Paper-Based Analytical Devices – μPADs
to measure blood levels of ALT (alanine aminotransferases) and AST (aspartate aminotransferase) and control
40
ALT
This enzyme is found mainly in your liver. Smaller amounts of ALT are in your kidneys and other organs, too.
Your body uses ALT to break down food into energy. Normally, ALT levels in the blood are low. If your liver is damaged, it will release more ALT into your blood and levels will rise. (ALT used to be called serum glutamic-pyruvic transaminase, or SGPT).
41
AST
is found in the highest concentrations in your muscles, heart, red blood cells, and liver. A small amount of AST is typically in your bloodstream. Higher-than-normal amounts of this enzyme in your blood may be a sign of a health problem. Any AST level below 40 units per liter (U/L) in adults isn’t uncommon.
AST levels increase when there’s damage to the tissues and cells where the enzyme is found. Elevated levels indicate that there is a certain amount of damage in that area. AST levels can rise as soon as 6 to 10 hours after damage occurs and remain high for months, depending on the cause. It’s normal for AST levels to be elevated in children from birth up to 2 years old.
Doctors commonly use the AST test to check for liver diseases, such as hepatitis. It’s usually measured together with alanine aminotransferase (ALT). The AST-to-ALT ratio can help your doctor diagnose liver disease. This ratio can determine if there’s been damage to your liver as opposed to damage to your heart or muscles.
42
Future of healthcare
Healthcare will become more personalized, the role patients play in the care of their health will increase
Research will bring about a new realm of precision and efficiency to the way information is transmitted, interpreted and used in medicine
Due to miniaturized devices and wireless communication
small sample of blood from a finger prick, analyzed to change colors in response to metabolic irregularities
Low-cost diagnostic imaging devices for POC make affordable diagnostic imaging more widely available, especially in remote or rural communities and small hospitals
43
POCt near to patient and medical care is far away
patients should use it
44
circulating tumors cells and cell-free DNA
circulating tumor cells
- applications
- methods of detection
- advantages
- disadvantages
- Singapore Perspective
- Asia Perspective
circulating cell-free DNA
- epigenetic alteration
45
Circulating tumor cells
Rare cancer cells released from a tumor into the bloodstream or lymphatic system
46
What do CTCs do in circulation ?
Remain loose
Cluster together or
Attach themselves in new tissues - metastasis (cancer spread to a different part of the body from where it started)
47
Applications of CTCs
cancer diagnosis
cancer treatment
through enumeration or molecular characterization
48
Enumeration of CTCs
- guide prognosis
- predictive and/or pharmacodynamic biomarker
- select patients for adjuvant chemotherapy
- detection of recurrent disease
- aid in diagnostic processes
49
real-time biopsy using CTCs
"real-time biopsy' (examine a tissue in real-time)
- expressions of HER2 has been detected in CTCs in metastatic breast cancer patients in cases where primary tumors were negative at original diagnosis
-- suggesting change in biological activity over time and may justify treatment with the HER2-receptor antagonists such as trastuzumab in patients who previously would not have been eligible
- Four of the nine patients were treated with trastuzumab containing therapy, three of whom showed evidence of complete or partial response.
50
molecular characteristics of CTC
- help researchers understand the prognostic and predictive features of the cancer
- determine if treatment would be efficient
- detection of treatment resident profiles
- improve understanding of mechanisms of biological processes
- discover and identify new targets for therapeutic manipulation
51
Methods of CTC detection
nucleic acid based
- detection of specific DNA or RNA sequences differentially expressed by tumor cells with RT-PCR (reverse transcriptase polymerase chain reaction)
cytometric approaches
- allows for enumeration and visualization of morphology of cells using fluorescence microscopy or immunohistochemistry
- allows for further analysis using techniques such as fluorescent in situ hybridization
- use immunostaining profiles to identify and characterize CTCs
52
Cytometric approaches for CTC detection
These assays need to be highly sensitive, highly specific and highly reproducible if they are to be useful in the clinical setting and used to make patient treatment decisions
most methods use an initial enrichment step to optimize the probability of rare cell detection, achievable through immunomagnetic separation, centrifugation or filtration
53
workflow for nucleic acid based techniques and tools
1) nucleic acid extraction/purification
2) nucleic acid quality and quantity determination
3) amplification-based techniques
4) detection/scoring
5) reporting
54
DNA extraction principle
manual
- lysin
- protein precipitation
- DNA precipitation
- wash with ethanol
- DNA hydration
automatic
- lysin
- magnetic particles added to samples
- DNA binds to magnetic particles
- magnetic separation
- wash
- magnetic separation
- elute
55
Droplet digital PCR
1. Process PCR-ready samples, combine DNA/RNA sample and primers and probes with one of the bio-rad ddPCR supermixes
2. load the ddPCR reaction mix into the wells of a droplet generator cartridge
8 x 20,000 droplets are generated from each run in the QX100 or QX200 droplet generator
Target DNA and background DNA are randomly distributed in droplets
3. Transfer the droplets to a 96-well PCR plate and seal the plate. Run the PCR protocol
4. Read and analyze the results. After PCR, load the 96 well PCR plate into QX100 or QX200 droplet reader. Positive and negative droplets in each sample are read. Analyze concentrations with QuantaSoft software
56
Advantages of nucleic acid based assay used in CTCs
- highly sensitive in particular with multi-marker survey
- can be performed without enrichment steps but at expense of sensitivity
- quantitative RT-PCR permits relative quantification
57
Advantages of cytometric approaches used in CTCs
- cells directly visualized by immunohistochemistry or immunofluorescence allows for evaluation of morphology and CTC enumeration
- cells can be extracted for molecular characterization (FISH, RT-PCR)
- has greater specificity than nucleic acid methods
58
Disadvantages of nucleic acid based methods used in CTCs
- cells cannot be visualized directly for the morphology or enumeration
- difficult to standardize techniques across laboratories
- no transcripts purely specific for tumor cells thus high false positive rate
59
Disadvantages of cytometric approaches used in CTCs
- detection depends on epithelial or tumor marker expression
- no pure CTC marker exists
- false-positive cells may be enriched
- current technique probably less sensitive than nucleic acid methods
60
CTCs - Singapore Perspective
```
Clear Bridge Bio Medics (CBB)
Specializes in novel platforms with applications in oncology research and diagnostics
Two products
- clear cells FX1 system
- CTChip
```
61
Clearcell FX1 system
provides a label free means of circulating tumor cells (CTC) enrichment that offers a myraid of possibilities for downstream analysis on the output CTCs
aims to provide the next generation of non-invasive "liquid biopsy" approaches for cancer screening, diagnostics, staging, personalized medicine and treatment monitoring
62
CTChip FR
CTChip FR
the microfluidic biochip captures CTCs based on inertia characteristics such as size and deformability, relative to other blood components, by using dean flow fractionation
through the dff process, the cells are focused within the microfluidic channels of the CTChip FR, with larger cells along the inner wall and the smaller cells away from it.
The label-free approach ensures effective, continuous and quick separation while retaining cell viability thus lending itself as a myriad of downstream applications
63
CTCs Asia Perspective
Menarini Silicon Biosystems
- aiming to become the leading provider of diagnostic products and services which will be able to inform cancer patients about the most optimial therapeutic diecision
- purchased all assets and relevant business related to the CellSearch Circulating Tumor Cell System in 2017.
64
CTCs Asia Perspective
CellSearch Circulating Tumor Cell System
A diagnostic test that is able to determine the prognosis of patients with metastatic breast, colorectal or prostate cancer
The first and approved CTC test for cancer patients in cancer
65
CellSearch Circulating tumor cell system
Intended for the immunomagnetic selection, identification and enumeration of circulating tumour cells (CTCs) in the blood
Some of the kits components include
- ready to use ferrotluid-based capture reagent and immunofluorescent reagents for 16 complete tests
- specially designed cartridges for optimal CTC isolation and analysis
66
Circulating cell-free DNA (cfDNA)
small DNA fragments found circulating in plasma, serum, blood, and other bodily fluids
1) derived from apoptotic cells in the plasma
- mononucleosomal (approximately 170bps)
- dinucleosomal (approximately 300bps)
2) derived from necrotic cells
- larger fragments (>1000bps)
3) possible applications in
non-invasive methods for diagnosis
monitoring of diseases
67
cfDNA in healthy people
the levels of cfDNA in plasma/serum is generally low, ranging between -0-50ng/ml
68
cfDNA increase
during pregnancy, illness and exacerbation of tissue
the levels of cfDNA generally increase
during pregnancy cDNA derived from fetus is often present circulating in maternal plasma and has been utilized in pre-natal screening for trisomies and other fetal conditions.
in cancer patients, mutations in the RAS genes were among the first alterations reported in cfDNA, and has been studied as a potential biomarker for monitoring tumor progression and recurrence, response to therapy. Other cfDNA alterations might have value for monitoring transplant rejection, diabetes, autoimmune and cardiovascular diseases.
69
Apoptosis and cfDNA
Apoptosis is a feature of villious trophobiast throughout pregnancy and is an essential feature of placenta invasion, cytotrophoblast fusion, and syncytiotrophoblast function as well as potentially playing a role in maternal immune tolerance.
apoptosis in placenta villi changes throughout pregnancy, this makes cfDNA
70
cfDNA in maternal circulation
Both material and fetal cell-free DNA are present in plasma fraction
Both maternal and fetal cells are present in cellular fraction
<1% of total DNA (cell-free and cellular) in maternal circulation is fetal
For every 1ml of maternal blood, an average of 1 cell is fetal
Between 4-30% of cell-free DNA (cfDNA) in maternal ciurculation is fetal (cfDNA)
Maternal circulation
- Adiopocytes
- white blood cells
Fetal
- placental cells (trophoblasts in the maternal circulation)
71
Epigenetic alterations in circulating cell-free DNA (cfDNA)
Epigenetic marks can distinguish the tissue of origin of the cfDNA
- useful for diagnosing or monitoring multiple diseases that cannot be distinguished by genetic differences or diseases that dont have distinct genetic features
eg, methylation and nucleosome positioning
72
Epigenetic marks
A change in the chemical structure of DNA that does not change the DNA coding sequence. e,g methylation or changes to proteins called histones
2 studies suggest that epigenetic marks could distinguish the tissue of origin of cfDNAs.
hence, far distinctions of tissues contributing to cDNA has relied on genetic differences between them.
e.g compare tumors from normal and compare cfDAN from fetus and mother
73
Insulin gene promoter (methylation example)
insulin gene promoter has previously been reported to be unmethylated in beta-cells of type 1 diabetes patients, but methylated in other tissues
Unmethylated INS promoter in cfDNA derived from beta cells of type 1 diabetes patients were detected whereas healthy individuals had undetectable or negligible amounts
spot diabetes from the cfDNA
74
Nuclesoome positioning (example)
useful for the classification of cancers during early diagnosis
found that nucleosome maps derived from these were very distinct
- maps derived from the cfDNAs of healthy individuals correlated with hematopoietic cells which are consistent with myeloid and lymphoid cells that are the major contributing cells to the cfDNA in healthy individuals
- maps derived from cfDNA of cancer patients contain cfDNA that correlated with non-hematopoietic cells, often correlating with cell types corresponding to same cancer type
75
Consumer genetics
consumers have direct access to informative biotech applications
broad range of tests offered by companies to provide reports on an individual's ancestry, health and traits.
76
Single Polynucleotide Polymorphism
A DNA sequence variation that occurs when a single nucleotide is altered in a genome sequence
must be present in 1% of population
used to be the only way to test people's genome
with the completion of human genome project, full-genome sequence is offered to customers
77
How scientists identify SNPs ?
primer extension is a method of detecting these SNPs
1. add primers which end at SNP position
2. add nucleotides to extend the primer, nucleotides will be added to the end of the primer only if sequence is an exact match
3. compare the lengths of the products using gel electrophoresis
78
Linked and Causative SNPs
Linked SNPs (outside of genes) - no effect on protein production or function
Causative SNPs in gene (in genes) - non-coding SNPs changes the amount of proteins produced while coding SNPs changes amino acid sequence
79
Effects of SNPs
most SNPs do not have effect on health/development
some of these genetic differences can be used in the study of human health such as to predict a person's response to particular drugs or risk of developing certain disease
80
Hypolactasia/lactose intolerance/lactase deficiency (applications of SNPs)
LCT gene responsible for lactase productions
lactase helps to digest lactose
most people can digest lactose
but 75% of the world population lose this ability while the others can digest lactose into adulthood
81
2 SNPs associated with the primary haplotype associated with hypolactasia
Rs4988235
Rs182549
82
Rs4988235
variant in intron3
located in the MCM6 gene but with influence on the LCT gene
the genotype LCT-13910CC, when the lactase-persistent allele (LCT-13910T) is absent, is consistent with lactose maldigestion
Mag 2,5, likely to be lactose intolerant as an adult
Mag 1,1 can digest milk
83
Rs182549
variant in intron9
located in the MCM6 but with influence on the LCT gene
Mag, 2 possibly lactose intolerant
Mag, 1 can digest milk
84
2 SNPs associated with Increased risk of alzheimers
Rs429358
Rs7412
85
Rs429358
located in the fourth exon of the ApoE gene, affects the amino acid at position 130 of the resulting protein
86
Rs7412
If the allele is (C) and the same chromosome also harbors the rs7412(C) allele, the combination is known as an APOE-ε4 allele.
The APOE-ε4 allele has a strong influence on the risk of Alzheimer's disease.
23andMe (v3 chip) tests for this SNP.
87
DTC (Direct-to-Consumer) Genetic Testing (Traditional)
1. Available only through healthcare providers
2. Tests are ordered from a laboratory and samples are collected from a patient
3. Healthcare providers will interpret the results and advise accordingly
88
DTC (Direct-to-Consumer) Genetic Testing (Current)
1. Genetic test kits are marketed to the public via television, print advertisements, internet..etc
2. Consumers purchase the kits directly from the company
3. Samples are collected at home with the kit and sent back to the company’s laboratory
4. Consumers are notified of their results online or via mail / telephone
89
DTC debate
Yes
Every individual has the right to learn about their own DNA even if preventive measures can’t be undertaken
Lowers the need for and cost of medical checkups since consumers can learn about their genetic profile without the aid of healthcare professionals
It is a faster and more private way for individuals to obtain information about their genetics, which includes disease predisposition and its carrier status
No
Individuals should be learning about their DNA from doctors / genetic counselors→ ensures that results are clearly explained
Uncertainty regarding the accuracy and usefulness of the tests
The psychological and emotional status of the participant cannot be monitored due to the life-altering nature of results offered
90
Reasons why completely replacing medical professionals with DTC kits is not practical
1. do not account for demographic and geographical differences
2. companies are unable to provide accurate analysis of results personalized to individual medical history
3. unaccountability for environment, lifestyle and hereditary factors
Hence, it is too generic to replace medical professionals with DTC kits
91
3 reasons people choose DTC testing
1. identity seeking - identify their ancestry, paternity, ethnicity, plays a role in the search to define who i am
2. complements current healthcare services - diseases risk-testing appeals to physicians and provides additional knowledge that can complement current diagnosis of patients
3. constant search for a better lifestyle - increased curiosity about their own genetic makeup, learn about potential future diseases
92
23andMe saliva based DTC genetic testing
1. order a saliva collection kit from the official website
2. follow kit instructions and mall sample back to lab
3. check out the results report online after 6-8 weeks
93
23andMe temporary ban
FDA banned the company 's genomic service for a lack of compliance in 2013 as the DNA kits do not classify as a medical device
Company failed to prove the reliability of the kits
- the personalized health analysis did not validate
- company's interpretation of the results might encourage patients to treat themselves and medicate inaccurately, leading to fatality
94
23andMe : Moving forward
Allowed to sell personal genome kits after gaining FDA approval
- the company has proved accurate results by discovering consistent links between certain gene variants and 10 different diseases
- 23andMe is now allowed to sell tests that help consumers assess their genetic risk regarding these 10 diseases
examples: parkinson's disease, late-onset alzheimers's disease, celiac disease
parkinson - nervous system disorder impacting movement
late-onset alzheimer's disease - progressive brain disorder that destroys memory and thinking skills
celiac disease - disorder resulting in the ability to digest gluten
95
Other leading companies beside 23andme in direct-to-consumer genetic testing
color genetics
- innovative, fully automated laboratory for high speed computation and analysis
- analyzes 19 genes that have a role in hereditary breast cancer and ovarian cancer
DNAfit
- works with ancestory.com's wide database to increase accuracy of results
- offers personalized diet and fitness recommendations
