Cytogenomics

Question 1

For most hematologic malignancies _________ analyses, _______, and _____are essential components of the diagnostic workup that guides clinical care.

Answer 1

karyotype, FISH and CMA

Question 2

NCCN guidelines for hematologic malignancies include the following- ________analyses (karyotype + FISH) the analysis of chromosomal structural variations by cytogenetics, fluorescence in situ hybridization (FISH), or __________ ____________ sequencing

Answer 2

cytogenetic
whole genome

Question 3

Name 6 things cytogenetics is missing:

Answer 3

1. Small CNVs
2. Structural variants
3. SNVs, deletions and duplications
4. Location of CNV gains
5. Mosaicism
6. Repetitive regions

Question 4

Karyotype has a limited resolution of ____ - ______ Mb

Answer 4

5-10 Mb

Question 5

CMA – reporting______ kb for loss and >_____ kb for gains - reporting of smaller findings in clinically significant regions

Answer 5

200 kb (loss)
400 kb (gain)

Question 6

ACMG in 2021 strongly recommended that _____/____ be considered as a first- or second-tier test for patients with CA/DD/ID

Answer 6

WES/WGS

Question 7

Trio exome sequencing has a sensitivity of ~_____________% for severe single gene variants in the NICU

Answer 7

37

Question 8

WGS is cost ___________ in the NICU

Answer 8

effective
- decreases morbidity and hospitalization costs

Question 9

FISH probes have to be ____________ for chromosomal aberration

Answer 9

specific

Question 10

Chromosomal microarray sensitivity is limited to ________gains or losses
and cannot identify __________ within the genome

Answer 10

large
location

Question 11

Chromosome analysis (karyotype) is still the gold standard in heme as molecular cannot resolve ___________ variants and complex ______________

Answer 11

structural variants
complex rearrangements

Question 12

CMA identifies ______________s not identified on sequencing as well as ____________ and genome complexity

Answer 12

CNVs
AOH/LOH

Question 13

~50% genome is repetitive sequences

Question 14

Optical genome mapping (OGM) can detect indels of _________ bp or ___________ bp for mosaic samples

Answer 14

500 bp
5000 bp (mosaic)

Question 15

OGM can detect __________ inversion and duplications of ___________ bp

Answer 15

30,000 bp

Question 16

OGM can detect balanced and unbalanced translocation of ____________ bp

Answer 16

50,000 bp

Question 17

OGM cannot detect ___________ translocations, ___________ or ____________

Answer 17

balanced translocations, triploidy or AOH/LOH

Question 18

OGM has limitations due to lack of knowledge of structural variants and ______ databases

Answer 18

required

Question 19

Long read sequencing improvements of short read sequencing includes detection of __________ variants and ________ regions

Answer 19

structural variants
(highly) repetitive regions

Question 20

The main disadvantages for long read sequencing include lower ____________, higher ________ , less mature __________

Answer 20

lower accuracy
higher cost
less mature bioinformatics

Question 21

WGS, OGM and LRS all have ________________ challenges

Answer 21

interpretation

Question 22

Methylation (and base modification) and phasing are currently capable with ___________ sequencing

Answer 22

long read sequencing (LRS)