Exam 3

Question 1

true or false: all cells that express class 2 proteins also express class 1 proteins

Answer 1

true

Question 2

What is the gold standard for HPV detection

Answer 2

molecular detection

Question 3

ThinPrep PresercCyt cervical PAP smear
SurePath specimen
(both can used for cytology & testing)

Answer 3

Specimen types for HPV

Question 4

alleles named in sequential order as they are discovered
EX: “A25:03” third specific allele, 03, of the HLA-A25 family of alleles

Answer 4

revised nomenclature for HLAs

Question 5

how many molecules were sequences for given read length

Answer 5

read length

Question 6

shows how many reads have accumulated per each of the detected barcode (indices) on the run

Answer 6

barcode hits

Question 7

describes how much data has already been base called, how much has passed quality filters

Answer 7

cumulative output

Question 8

How does read length impact sequencing analysis?

Answer 8

Longer reads improve genome assembly and structural variant detection, while shorter reads enhance accuracy in repetitive regions.

Question 9

plates loaded w/ ab against known HLA types
the donor or recipient lymphocytes placed in wells

Answer 9

complement dependent cytotoxicity (CDC) test

Question 10

how do different HLA typing methods compare in resolution?

Answer 10

Serological methods provide low resolution, PCR-based methods offer intermediate resolution, and sequencing methods provide high-resolution HLA typing.

Question 11

-added to DNA fragments before PCR amp to remove duplicates

Answer 11

unique molecular identifiers

Question 12

multiple sections of the circle representing the relative quantity of each organism

Answer 12

multiple source specimen

Question 13

High cytotoxicity
cells have surface antigens matching the known antibody in the well

Answer 13

interpretation of CDC

Question 14

-voltage is constant during sequencing but changes during pore scans
-voltage controls whether DNA molecules are pulled though pore

Answer 14

bias voltage history

Question 15

incomplete reference genomics in the bioinformatics workflow

Answer 15

unknown calls

Question 16

What is a Q-score in nanopore sequencing?

Answer 16

A Q-score indicates basecalling accuracy; a Q10 score equals 90% accuracy, while higher Q-scores imply greater confidence.

Question 17

responsible for load of HPV in cervical cancer

Answer 17

E6 & E7

Question 18

too many small fragments
too little DNA
poor adapter ligation

Answer 18

problem with the library

Question 19

positive crossmatch
recipient serum kills donor lymphocytes
donor is not a possible candidate

Answer 19

interpretation of crossmatching

Question 20

-visual representation of the taxonomic composition of the sample
-hierarchal ranking
-species on the outside layer

Answer 20

sunburst taxonomy graph

Question 21

tissue and blood cells of a separate genetic origin

Answer 21

full chimera

Question 22

non-enveloped, double-stranded circular DNA genome
-early expressed
-late expressed
-long control region

Answer 22

genome of HPV

Question 23

Which transplant requires the highest level of HLA typing?

Answer 23

bone marrow

Question 24

disrupts pRB, causing stimulation of cellular DNA synthesis and cell division

Answer 24

E7 protein

Question 25

What are squiggles in nanopore sequencing?

Answer 25

Squiggles are electrical signal traces generated as DNA bases pass through the nanopore, used for basecalling.

Question 26

Which two HLAs classes have antigen presenting proteins?

Answer 26

Class 1 and 2

Question 27

What molecular methods are used to identify HLA types?

Answer 27

Techniques include sequence-specific oligonucleotide probe hybridization (SSOP), sequence-specific PCR (SSP-PCR), and direct DNA sequencing.

Question 28

region of interest amplified using PCR Low resolution

Answer 28

Sequence-specific oligonucleotide probe hybridization (SSOP)

Question 29

Which transplant is associated with BK virus?

Answer 29

kidney

Question 30

How are HLA alleles named?

Answer 30

The WHO nomenclature assigns names based on gene (e.g., HLA-A), followed by an asterisk and a numerical code indicating allele specificity (e.g., HLA-A*26:01).

Question 31

the detection units in a flow cell, each containing multiple pores, but only one pore per channel is active at a time.

Answer 31

Channels

Question 32

variant present in small proportion of the cell which indicates its not driving the growth of tumors

Answer 32

low VAF

Question 33

If HPV is persistent what will it lead to?

Answer 33

cervival cancer

Question 34

sequencing available recovering inactive (dead pore)

Answer 34

channel classifications

Question 35

more mapped reads= better identification confidence

Answer 35

number of reads per barcode

Question 36

how fast the molecule is moving through the pore

Answer 36

translocation speed

Question 37

all of the circle showing the same species

Answer 37

single source specimen

Question 38

What's include in FASTQC report include

Answer 38

-base sequence quality -sequence quality scores -base GC content -base N content -sequence length distribution -sequence duplication levels

Question 39

what can affect a Phred score

Answer 39

sequencing chemistry, read length, and the instrument used for sequencing

Question 40

How are engraftment success and failure determined?

Answer 40

By analyzing the proportion of donor-derived DNA using STR analysis.

Question 41

related to the accuracy of base calling

Answer 41

quality scores

Question 42

recipient serum (antibodies) tested against donor lymphocytes

Answer 42

crossmatching

Question 43

Cancers of the oropharynx, cervix, vulva, vagina, anus & penis

Answer 43

high risk HPV

Question 44

how to calculate VAF

Answer 44

dividing the number of variant reads by the total number of reads MUST BE EXPRESSED AS A PERCENT

Question 45

1.Amplicons denatured and spotted onto a membrane 2.labeled oligonucleotide probes are designed to hybridize to specific HLA alleles 3. Spots detected from chemiluminescent or calorimetric signal

Answer 45

Steps for SSOP

Question 46

50 pores

Answer 46

minimum QC criteria for a flongle

Question 47

variant present in a large proportion of cells which indicates that its driving the growth of the tumor

Answer 47

high VAF

Question 48

Highest resolution distinguish between one-nucleotide difference

Answer 48

direct DNA sequencing

Question 49

What can a Phred score exclude

Answer 49

low quality base calls that have high probability of being incorrect

Question 50

What is the MHC locus and its function?

Answer 50

The MHC locus is a group of genes on chromosome 6 that encodes human leukocyte antigens (HLAs), which are essential for immune system function and transplant compatibility.

Question 51

What does MinKNOW software monitor during sequencing?

Answer 51

It tracks sequencing quality, detects errors, and monitors trends like voltage, temperature, and pore status.

Question 52

report shows quality information and gives read length and base yields

Answer 52

Metagenomics report

Question 53

What do you want to do to PCR duplicates

Answer 53

remove them from the sequencing sample because it will lead to uneven distribution and artifacts will be removed

Question 54

process of attaching functional information to the genetic sequences

Answer 54

variant annotation

Question 55

What is a MUX/Pore scan?

Answer 55

A diagnostic scan that assesses active, recovering, and inactive pores in a sequencing run.

Question 56

What type of resolution is needed for bone marrow/stem cell transplants

Answer 56

high resolution

Question 57

set of particular alleles on the same chromosome inherited together as a block

Answer 57

Haplotype HLA inheritance

Question 58

What are informative and non-informative loci?

Answer 58

Informative loci distinguish donor and recipient cells, while non-informative loci appear identical in both.

Question 59

-viral capsid protein -target for amp & detection for HPV

Answer 59

L1 gene

Question 60

-amplifies only specific alleles -control amplicons and allele-specific amplicons can be resolved by gel electrophoresis

Answer 60

sequence specific PCR (SSP-PCR)

Question 61

HLA-A*26:03

Answer 61

high resolution

Question 62

examines how many of the wells are one working pores, multiple working pores, zero pores, unavailable, or saturated

Answer 62

pore scan check

Question 63

in the nucleus but outside the chromosome

Answer 63

benign HPV

Question 64

allows for real-time base calling and alignment according to the desired bioinformatics pipeline

Answer 64

EPI2ME

Question 65

reflects the balance between informative sequence data and the noise that is not informative or hard to interpret

Answer 65

signal to noise ratio

Question 66

What is the role of alignment in sequencing?

Answer 66

Aligning reads to a reference genome helps identify mutations, structural variations, and microbial species.

Question 67

What does high Phred score indicate

Answer 67

low probability of an incorrect base call

Question 68

what are some problems with transplants

Answer 68

rejection and graft vs. host disease

Question 69

High resolution focus on most polymorphic loci in the MHC use whole blood from EDTA tube

Answer 69

DNA-based typing

Question 70

What strains are protected against in the HPV vaccine?

Answer 70

high and low risk strains

Question 71

one read at a time, looking at reference genome & figuring out when read aligns

Answer 71

alignment

Question 72

only recipient cells are found after transplant

Answer 72

failed transplant

Question 73

Molecules expressed on the surface of all nucleated cells in the body + platelets

Answer 73

HLA class 1

Question 74

What are ethical concerns in HLA typing and transplantation?

Answer 74

Issues include donor consent, false paternity discovery, and equitable organ allocation.

Question 75

molecules expressed on the surface of "professional" antigen-presenting cells of the immune system (B-cells, lymphs, monocytes, macrophages, & dendritic cells)

Answer 75

HLA class 2

Question 76

measure of how common a particular variant is within a population of cells

Answer 76

variant allele fraction (VAF)

Question 77

What diseases are associated with MHC

Answer 77

autoimmune disease

Question 78

measure of the quality of a base made by an NGS platform

Answer 78

Phred score

Question 79

HLA-A*26 HLA-A

Answer 79

low resolution

Question 80

How to determine who cells are whose?

Answer 80

STR analysis by fragment analysis

Question 81

oncogene __ products interacts with p53

Answer 81

E6 gene

Question 82

reagent serum for known anti-HLA antibodies are used that recognize specific HLA loci or antigens

Answer 82

traditional typing (serological analysis)

Question 83

genital warts

Answer 83

low risk HPV

Question 84

-used for sorting DNA/RNA sequences -test based format for storing reads including quality values for each base

Answer 84

FASTQ

Question 85

What is the role of the MDx laboratory in organ and bone marrow transplantation?

Answer 85

The MDx laboratory performs HLA typing to match donors and recipients, monitors engraftment success, and detects potential transplant rejection or graft-versus-host disease.

Question 86

signal trace when each base interrupts the electrical potential of the membrane

Answer 86

squiggles

Question 87

How is STR analysis used for post-transplant monitoring?

Answer 87

Short Tandem Repeat (STR) analysis differentiates donor and recipient DNA to assess engraftment success.

Question 88

What are some reasons for non-uniform coverage?

Answer 88

sequencing bias, library preparation bias, mapping bias, sampling bias, experiment design

Question 89

detect patients who are at risk for developing cervical dysplasia and cervical cancer

Answer 89

HPV clinical utility

Question 90

donor and recipient cells are in found in patient sample

Answer 90

mixed chimera

Question 91

individual with genetically distinct cell populations from donor and recipient sources

Answer 91

chimera

Question 92

What is full chimerism vs. mixed chimerism?

Answer 92

Full chimerism means only donor cells are detected, while mixed chimerism indicates a mix of donor and recipient cells.

Question 93

cells from terminal state go to active state

Answer 93

viral replication

Question 94

-dont test below age 25 -cant distinguish between transient & persistent infections -HPV does not = cervical cancer -controversy: HPV is the sole screening method for cervical cancer risk

Answer 94

HPV testing considerations

Question 95

voltage issues air bubbles temp fluctuations

Answer 95

problems with a flow cell

Question 96

What is translocation speed?

Answer 96

The speed at which DNA molecules pass through a nanopore, affecting sequencing efficiency and accuracy.

Question 97

basal cells to mature keratinocytes -viral DNA is replicated -capsid protein synthesized -viral DNA release occurs

Answer 97

HPV life cycle

Question 98

what will cause low signal to noise ratio

Answer 98

background noise is loud meaning artifacts are being sequenced

Question 99

What factors can cause errors in HLA typing?

Answer 99

Contamination, low DNA quality, ambiguous allele calls, and reagent issues can affect results.

Question 100

What are the genomic features of HPV?

Answer 100

HPV is a non-enveloped, double-stranded circular DNA virus with early-expressed genes, late-expressed genes, and a Long Control Region (LCR).

Question 101

What are the most common high-risk HPV strains?

Answer 101

HPV 16 and HPV 18 are the most common high-risk strains associated with cervical cancer.

Question 102

What is the role of the E6 and E7 genes in HPV infection?

Answer 102

E6 degrades the tumor suppressor p53, while E7 disrupts the retinoblastoma protein (pRB), leading to uncontrolled cell division.

Question 103

How does HPV progress from infection to cancer?

Answer 103

HPV initially exists in an episomal state but integrates into the host genome in advanced stages, leading to cancerous transformation.

Question 104

What are the molecular methodologies used for HPV testing?

Answer 104

Molecular methods include hybrid capture (signal amplification), transcription-mediated amplification, and real-time multiplex PCR for strain typing.

Question 105

What are the clinical applications of HPV testing?

Answer 105

HPV testing is used for cervical cancer risk assessment, primary screening, and co-testing with Pap smears.

Question 106

What are the strengths of HPV testing?

Answer 106

High sensitivity, ability to detect high-risk strains, and strong predictive value for cervical dysplasia.

Question 107

What are the limitations of HPV testing?

Answer 107

Cannot distinguish between transient and persistent infection, and a positive result does not guarantee cancer.

Question 108

What are the specimen types used for HPV testing?

Answer 108

ThinPrep and SurePath cervical Pap smear specimens.

Question 109

Why is HPV testing not recommended for individuals under 25?

Answer 109

HPV infections are common and often clear naturally in younger individuals without causing cervical dysplasia.

Question 110

component of a FASTQ report

Answer 110

read identifier nucleotide sequence confidence score

Question 111

total number of reference sequence bases for which reads from a sample have been aligned

Answer 111

coverage