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Mol Bio Lab > Guidance for molecular clinical laboratory > Flashcards

Guidance for molecular clinical laboratory Flashcards

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1
Q

What are the gals of molecular diagnosis procedure

A
  1. select the right test for each patient
  2. generate accurate, clinically relevant results to optimally influence clinical care
  3. Conserve health care resources
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2
Q

enumerate the three division of all molecular diagnosis workflows

A

pre analytical, analytical, and post analytical

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3
Q

its standards aim at quality, format, and amount of specimen/sample which should be documented in detail

A

pre analytical

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4
Q

this considers the proof of these aspects, concerning DNA/RNA extraction, quantification, and purity determination via fluorometry or spectrophotometry

A

analytical standards

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5
Q

this mainly focuses on the documentation and bioinformatics process

A

post analytical

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6
Q

accession numbers are to be allocated to samples as per which ISOs?

A

ISO 15189 and ISO9001

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7
Q

what should SOPs follow?

A

ISO 15189 and any national guidelines

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8
Q

T or F

use of fixed tissue that was previously frozen is advisable as it yields better results

A

F (not advised)

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9
Q

what is the best fixing reagent

A

formaline

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10
Q

The process of removing calcium from a bone to make it softer for processing

A

decalcification

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11
Q

Why should a molecular biology laboratory staff be trained and highly skilled in the pre analytical phase

A

because mol bio specimens are highly variable

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12
Q

What should labs validate for specimen acceptability?

A

all potential specimen types and establish criteria

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13
Q

Laboratories must establish a ________ and ________ workflow for nucleic acid quantitation to guarantee accurate and reproducible results

A

standardized and cost-effective

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14
Q

The _____________________________ must be well developed to clearly define pre analytical sample quality

A

quality control methods

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15
Q

This method should be highly avoided because it detects all nucleic acids

however, it is still commonly used in laboratories as it is cheaper

A

spectrophotometric methods

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16
Q

What is recommended over spectrophotometric methods?

A

double stranded DNA specific fluorometric quantitation methods

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17
Q

It is important to consider whether the testing would ________ or be ______ in addition to existing diagnostic tests

A

supplant or be conducted

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18
Q

What tests should you do first before running multiplex PCR to ensure presence of pathogen

A

bacterial culture and susceptibility testing

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19
Q

factors to be considered in the choice of analytical method (yes, need mo siya kabisaduhin)

A
  1. number of samples that require testing
  2. number of genes being tested
  3. percentage of mutations tested in each gene
  4. amount of tissue available
  5. degree of staff expertise
  6. equipment, and infrastructure required
  7. need of separation of stages in different compartments
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20
Q

when does ensuring good DNA/RNA quality start?

A

isolation and extraction

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21
Q

T or F

DNA/RNA samples must be permanently on ice and avoid repeated freeze-thaw cycles

A

T

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22
Q

T or F

majority of incubation steps must be kept at higher temperatures to inhibit possible nuclease activity

A

F (lower temps)

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23
Q

enumerate the special sample requesitions by pacific biosciences RS II

A
  1. double stranded format of DNA
  2. prevention of pH extremes (<6, >9)
  3. absence of chelating agents, detergents, divalent metal cations, denaturants and RNA)
    4 . Quality assessment should yield an OD260/280 ratio of 1.8 to 2.0 and an OD260/230
    ratio of 2.0 to 2.2,
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24
Q

what should be the quality assessment ratios be?

A

OD260/280 ratio of 1.8 to 2.0 and an OD260/230
ratio of 2.0 to 2.2,

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25
Q

what temp should DNA and RNA samples be stored at?

A

less than 20degrees Celsius or lower

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26
Q

PCR products should be stored at what temp?

A

less than 20degrees Celsius or lower

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27
Q

Sequencing libraries should be stored at what temp?

A

less than 20degrees Celsius or lower

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28
Q

T or F

DNA and RNA samples, PCR products, and sequencing libraries may be stored at the same freezer as they share the same storing temperatures

A

F

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29
Q

T or F

RNA is more stable than DNA or cDA

A

F (DNA>RNA)

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30
Q

T or F

DNA is more likely to survive more years than cDNA if stored properly

A

F (same lang sila HAHHAHA)

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31
Q

Device almost exclusively used for quality control in sequencing fragments

A

capillary gel electrophoresis

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32
Q

can be used to investigate fragment size distribution and final library quality assessment

A

capillary gel electrophoresis

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33
Q

device that offers fluorometric quantitation and checks sample quality

A

fluorometer

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34
Q

what does the fluorometer determine?

A

input DNA/RNA amount

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35
Q

T or F

The validation process assess the pre analytical and analytical phase only

A

F (including the molecular report)

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36
Q

A molecular diagnostic report should include which ________ or regions of
the ________ are investigated, information about the gene coverage, the
sensitivity of the detection, and the frequency of the detected
mutation.

A

genes

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37
Q

why is it essential to monitor the performance of all tests in the clinical laboratory?

A

ensure all measurable parameters remain within acceptable limits?

38
Q

Pertains to the timeliness of reports that is critical to patient care, and the basis of patient pathways in practice in individual hospitals

A

turnaround time

39
Q

Acceptability of longer turnaround time can permit _____________ or _______________to improve the cost effectiveness of
testing.

A

greater control of testing or batching of samples

40
Q

A molecular diagnostic report should convey _________the information the clinician needs to treat the patient on whom the test was performed, with sufficient information to allow correct __________of the result.

A

accurately
interpretation

41
Q

3 key areas that should be included in reports

A
  1. patient identification
  2. reporting style and content
  3. Interpretation
42
Q

How many sample identifiers in total should be in the request form and report?

A

3 sample identifiers
(2 patient id and 1 on the sample id)

43
Q

T or F
Long reports are always read in full. One page, or better still, single-screen reports
are preferred, provided that they are legible

A

F (rarely read in full)

44
Q

what should the report have if it’s more than 1 page long?

A
  1. appropriate patient identifiers in all pages
  2. number the pages
45
Q

T or F

For all tests, the percentage of the sample occupied by the target of the test
(e.g., neoplastic cells) is important.

A

F (some lang, not all tests)

46
Q

Ideally, the report should contain basic information about ______ for quality control.

A

fixation

47
Q

The __________of the individual taking responsibility for the test and ________
details is important, and some form of authorization with date

A

name and contact

48
Q

The type and extent of molecular analysis used should be described clearly to allow ________to request further testing if warranted by the clinical situation

A

oncologists

49
Q

these are also known as proficiency testing and are inevitable for monitoring a lab’s performance

A

External Quality assurance (EQA)

50
Q

One of the requirements to become accredited according to ISO _______
is to participate in EQA programs

A

15189

51
Q

It is necessary to periodically assess the analytical performance of molecular tests by __________, which will assist laboratories in monitoring their assays and improve assay performance and evaluation of results.

A

Inter-laboratory comparison

52
Q

this is necessary to ensure high assay
reproducibility and performance and enable detection and correction
of errors in daily practice.

A

internal quality assurance (IQA)

53
Q

Assays should be performed according to SOPs using appropriate _______ and _______ _________

A

positive and negative controls

54
Q

Who performs the control every shift change?

A

RMT

55
Q

______ is essential to take charge of
participation and performance in quality assurance schemes and to
organize internal and external audits.

A

laboratory quality managerR

56
Q

T or F

the lab quality manager does the control also

A

f

57
Q

_______is the critical guidelines to ensure comparability and exchange of experimental data to accelerate the innovation process and aid improvement of transferability, transparency, and
reproducibility of results.

A

standards

58
Q

Standardization can ________________, therefore enabling improved financial planning and scheduling and a possible expansion of services

A

potentially decrease cost

59
Q

The results gained from successful standardization of NGS might _______ to other fields in life sciences

A

transfer

60
Q

Enumerate the general NGS workflow

A
  1. prepare sequencing library
  2. Prepare and enrich template
  3. sequencing
  4. data analysis
61
Q
  • control input
  • Fragmentation and end-repair
  • size selection
  • library normalization / quantification
A

Prepare sequencing library

62
Q
  • Clonally amplified DNA template prepared
  • enriched
A

prepare and enrich template

63
Q

-create a run
- clean and initialize sequencer
- begin sequencing

A

sequencing

64
Q

Data quality check and analysis

A

data analysis

65
Q

T or F

Quality assurance is under quality control

A

F (baliktad)

66
Q

What should the quality assurance program contain?

A
  1. predetermined QC checkpoints for monitoring QA
  2. extensive documentation (used devices, reagent lot numbers, reagent expiration date, and any deviation from standard procedures)
  3. Methods for contamination identification at several stages within the diagnosis workflow
  4. documentation of all methods, reagents, instruments, and controls
67
Q

Laboratories must define and document _________or ________criteria for each step of the wet bench process, such as DNA/RNA
extraction, library preparation, and sequencing

A

acceptance or rejection

68
Q

_____and ____________, such as maintenance logs, must exist to demonstrate and provide evidence that all instrumentation and equipment are validated, operated, inspected, maintained, tested, and standardized to ensure optimal quality of assay results.

A

SOPs and supporting documentation

69
Q

All preventive maintenance and calibrations must be scheduled and performed at least as frequently as suggested by the ____________ to ensure continued accuracy, precision, and extended usable life of the equipment in EQA programs

A

equipment manufacturers

70
Q

______ must conduct all preventative maintenance and service per manufacturer specifications

A

staff

71
Q

Guidelines of preventive maintenance (summarized) go read the whole thing also :>

A
  1. staff must keep al equipment clean
  2. lab must do the standard daily/weekly / monthly routine maintenance and to record the task
  3. Written policy / procedure should be in place
  4. primary and backup instruments should be compared to each other to determine result consistency
72
Q

Calibration / maintenance of automatic pipettors every ____

A

6 months

73
Q

Calibration / maintenance of thermometers every ____

A

1 year

74
Q

Calibration / maintenance of centrifuge every ____

A

6 months

75
Q

We should record the temperature / freezer’s temperature every _____

A

every day

76
Q

we should establish tolerance limits for temperatures, carbon dioxide level, and humidity as applicable for which equipment?

A

incubators and water bath

77
Q

What do we use to measure centrifuge speeds?

A

tachometer

78
Q

When should the autoclave’s pressure and temperature be checked?

A

every year

79
Q

When is the autoclave’s sterilization efficiency measured?

A

weekly

80
Q

How is content processing verified with each autoclave batch?

A

heat sensitive tape

81
Q

where should the analytical balance be placed?

A

stable location

82
Q

what can be used to clean the BSC’s UV lamp

A

70% alcohol

83
Q

Calibration / maintenance of BSC every ____

A

1 year

84
Q

Calibration / maintenance of generators every ____

A

1 month

85
Q

Accreditation means that medical laboratories have been assessed against ___________ to demonstrate their competence, impartiality and performance capacity.

A

internationally recognized standards

86
Q

What is the international standard for accreditation?

A

ISO 15189

87
Q

What is the title of ISO 15189

A

“Medical laboratories – particular requirements for quality and competence”

88
Q

what is ISO 15189 based on?

A

ISO/IEC 17025 and ISO 9001

89
Q

All laboratories providing molecular diagnostic services should have laboratory accreditation according to_______ or their _______

A

ISO 15189 or their national equivalent

90
Q

steps of accreditation

A
  1. Opening briefing
  2. Examination of records
  3. Sample handling
  4. Interview with technicians
  5. Demonstrations of tests and techniques
  6. Examination of equipment calibration and maintenance
  7. Review of quality documentation
  8. Written report of assessor’s findings
  9. Closure meeting
91
Q

Accreditation can be granted for ______ years, but the NABs will perform surveillance visits to ensure that the laboratory continues to meet requirements, which is typically every ______

A

3-5 years
1 to 2 years

Mol Bio Lab (12 decks)

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