Cases in Laboratory Genetics and Genomics (LGG) Practice

Cases in Laboratory Genetics and Genomics (LGG) Practice instructs readers in the lab-based diagnosis of genetic conditions, including inborn and acquired disorders using cytogenetics and molecular genetics technologies. This entirely case-based book covers a wide range of genetic cases, from prenatal to postnatal and oncology genetic disorders which lab professionals and geneticists encounter daily in the diagnostic field. Each disorder discussed includes a section on clinical background, clinical indication, tests ordered, laboratory tests performed, test results, results with interpretations, future testing and recommendations, and references.

The book will help lab professionals understand and navigate clinical cases using an integrative approach, and thoroughly understand the methodologies and interpretations involved in high complexity genetic testing.

Cover image
Title page
Table of Contents
Copyright
Dedication
Contributors
Foreword
Preface
Acknowledgments
Part I: Inborn diseases
1: Multiple congenital anomalies and developmental delay
Abstract
Background
Case 1.1 Multiple congenital anomalies caused by an unbalanced translocation
Case 1.2 Recombinant chromosome 8 syndrome
Case 1.3 Multiple congenital anomalies caused by an unbalanced translocation and a deletion
Case 1.4 Diamond-Blackfan anemia
Summary of key learning points
References
2: Molar pregnancy
Abstract
Background
Case 2.1 Complete mole
Case 2.2 Partial mole
Summary of key learning points
References
3: Sex chromosomal abnormalities
Abstract
Background
Case 3.1 Female with 45,X/46,XY mosaicism
Case 3.2 Sex reversal
Case 3.3 Variant turner syndrome
Case 3.4 Indeterminate sex with an abnormal Y chromosome
Case 3.5 Klinefelter syndrome (47,XXY)
Case 3.6 Klinefelter syndrome variant (48,XXYY syndrome)
Summary of key learning points
References
4: Consanguinity
Abstract
Background
Case 4.1 Multiple congenital anomalies due to family history of consanguinity
Case 4.2 Multiple developmental disorders due to consanguinity and Charcot-Marie-tooth disease type 1A
Summary of key learning points
References
5: Uniparental disomy and imprinting disorders
Abstract
Background
Case 5.1 Prader-Willi syndrome
Case 5.2 Prader-Willi/Angelman syndrome
Case 5.3 Angelman syndrome
Case 5.4 Gaucher disease
Case 5.5 Uniparental disomy 7
Summary of key learning points
References
6: Pallister-Killian syndrome
Abstract
Background
Case 6.1 Pallister-Killian syndrome
Case 6.2 Pallister-Killian syndrome
Summary of key learning points
References
7: Fragile X syndrome
Abstract
Background
Case 7.1 Fragile X syndrome in a male with a full mutation
Case 7.2 Fragile X syndrome in a female with a full mutation
Summary of key learning points
References
8: Overgrowth syndrome
Abstract
Background
Case 8.1 Sotos syndrome
Case 8.2 Somatic overgrowth syndrome with PIK3CA mutation
Summary of key learning points
References
9: Contiguous gene syndrome
Abstract
Background
Case 9.1 Haploinsufficiency of A20 (HA20) with 3.4 Mb deletion
Case 9.2 Haploinsufficiency of A20 (HA20) with 11.7 Mb deletion
Case 9.3 Contiguous gene syndrome with duplication of 22q11.2q12.1
Case 9.4 Contiguous gene syndrome with duplication of 6q16.1q23.3
Case 9.5 DiGeorge/Velo-cardio-facial (VCF) syndrome (22q11.2 deletion syndrome)
Case 9.6 Contiguous gene syndrome with a deletion of 1q43q44
Summary of key learning points
References
10: Thrombosis
Abstract
Background
Case 10.1 Deep vein thrombosis
Summary of key learning points
References
11: Pharmacogenomics
Abstract
Background
Case 11.1 Overdose acetaminophen (APAP)
Summary of key learning points
References
Part II: Hematologic malignancies
12: Chronic myeloid leukemia
Abstract
Background
Case 12.1 Chronic myeloid Leukemia (CML) with t(1;9;22;15)(p32;q34;q11.2;q25)
Case 12.2 Chronic myeloid leukemia (CML) with t(9;22;17)(q34;q11.2;q24)
Case 12.3 Chronic myeloid leukemia (CML) with t(9;22)(q34;q11.2)inv(22)
Case 12.4 Chronic myeloid leukemia and acute lymphoblastic leukemia with t(9;22)(q34;q11.2)
Summary of key learning points
References
13: Myeloid/lymphoid neoplasms with eosinophilia and tyrosine kinase gene fusions
Abstract
Background
Case 13.1 Myeloid/lymphoid neoplasm (MLN) with FGFR1 rearrangement
Case 13.2 Myeloid/lymphoid neoplasm (MLN) with PDGFRA rearrangement (LNX1 Deletion by FISH)
Case 13.3 Myeloid/lymphoid neoplasm (MLN) with PDGFRA rearrangement (CHIC2 Deletion by CMA)
Case 13.4 Myeloid/lymphoid neoplasm (MLN) with PDGFRB rearrangement
Case 13.5 Myeloid/lymphoid neoplasm (MLN) with a variant PDGFRB rearrangement
Case 13.6. Myeloid/lymphoid neoplasm with JAK2 rearrangement
Summary of key learning points
References
14: Myelodysplastic/myeloproliferative neoplasms
Abstract
Background
Case 14.1 Chronic myelomonocytic leukemia (CMML)
Case 14.2 Myelodysplastic/myeloproliferative neoplasm with ring sideroblasts and thrombocytosis (MDS/MPN-RS-T)
Summary of key learning points
References
15: Myelodysplastic neoplasms
Abstract
Background
Case 15.1 Myelodysplastic neoplasms with excess blasts-2 (MDS EB-2)
Case 15.2 Myelodysplastic neoplasms: Refractory anemia with ring sideroblasts (RARS)
Case 15.3 High-grade myelodysplastic neoplasms (MDS)
Case 15.4 Myelodysplastic neoplasms with excess blasts (MDS EB-1) transforming to AML
Case 15.5 Myelodysplastic neoplasms: Refractory cytopenia with multilineage dysplasia (MDS-RCMD)
Summary of key learning points
References
16: Acute myeloid leukemia (AML)
Abstract
Background
Case 16.1 Acute myeloid leukemia (AML) with t(3;21)(q26.2;q22)/RUNX1::MECOM fusion
Case 16.2 Acute myeloid leukemia (AML) with t(6;9)(p22;q34)/DEK::NUP214 fusion
Case 16.3 Acute myeloid leukemia (AML) with t(9;11)(p21;q23)/KMT2A::MLLT3 fusion
Case 16.4 Acute myeloid leukemia (AML) with t(8;21;21)(q22;p13;q22)/RUNX1::RUNX1T1 fusion
Case 16.5 Acute myeloid leukemia (AML) with CEBPA double mutations
Case 16.6 Acute myeloid leukemia (AML) with a complex karyotype and TP53 mutation
Case 16.7 Acute promyelocytic leukemia (APL) with a typical PML::RARA fusion and FLT3-ITD mutation
Case 16.8 Acute promyelocytic leukemia (APL) with a variant ZBTB16::RARA fusion
Case 16.9 Acute promyelocytic leukemia (APL) with a cryptic PML::RARA fusion
Case 16.10 Acute myeloid leukemia (AML) with jumping translocations
Case 16.11 Acute myeloid leukemia (AML) with a complex karyotype and multiple mutations
Case 16.12 Acute myeloid leukemia (AML) with t(10;11)(p12;q23)/KMT2A::MLLT10 fusion
Case 16.13 Acute myeloid leukemia (AML) with t(11;19)(q23;p13.3)/KMT2A::MLLT1 fusion
Case 16.14 Acute myeloid leukemia with NUP98::KDM5A fusion
Summary of key learning points
References
17: Blastic plasmacytoid dendritic cell neoplasm (BPDCN)
Abstract
Background
Case 17.1 Blastic plasmacytoid dendritic cell neoplasm (BPDCN)
Summary of key learning points
References
18: Acute leukemias of ambiguous lineage
Abstract
Background
Case 18.1 Mixed phenotype acute (B/myeloid) leukemia (MPAL) with a complex karyotype
Case 18.2 Mixed phenotype acute (B/myeloid) leukemia (MPAL) with FLT3-ITD and other mutations
Case 18.3 Mixed phenotype acute (B/myeloid) leukemia (MPAL) with RUNX1 mutation
Summary of key learning points
References
19: Precursor lymphoid neoplasms
Abstract
Background
Case 19.1 B-lymphoblastic leukemia (B-ALL, Ph+) with T315I resistance mutation
Case 19.2 B-lymphoblastic leukemia (B-ALL, Ph+) with a complex karyotype
Case 19.3 Relapsed B-lymphoblastic leukemia (B-ALL, Ph−) with a complex karyotype
Case 19.4 B-lymphoblastic leukemia (B-ALL) with t(12;21)(p13;q22)/ETV6::RUNX1 fusion
Case 19.5 Ph-like B-lymphoblastic leukemia (Ph-like ALL) with CRLF2 rearrangement
Case 19.6 T-lymphoblastic leukemia (T-ALL) with t(10;11)(p12;q21)/PICALM::MLLT10 fusion
Case 19.7 T-lymphoblastic leukemia (T-ALL) with t(11;18)(p15;q12)/NUP98::SETBP1 fusion
Case 19.8 T-lymphoblastic leukemia (T-ALL) with t(1;14)(p32;q11.2)/TRA::TAL1 fusion
Case 19.9 T-lymphoblastic leukemia (T-ALL) with t(11;14)(p13;q11.2)/LMO2::TRD fusion
Case 19.10 Ph-like B-lymphoblastic leukemia (Ph-like ALL) with CRLF2 rearrangement and t(2;8)(p12;q24)/IGK::MYC fusion
Case 19.11 B-lymphoblastic leukemia (B-ALL) with t(1;19) (q23;p13.3)/TCF3::PBX1 fusion
Case 19.12 B-lymphoblastic leukemia (B-ALL) with iAMP21
Case 19.13 Ph-like B-cell lymphoblastic leukemia (Ph-like ALL) with IGH and CRLF2 rearrangements
Summary of the key learning points
References
20: Mature B-cell neoplasms
Abstract
Background
Case 20.1 Atypical B-cell chronic lymphocytic leukemia (CLL)
Case 20.2 Mantle cell lymphoma (MCL)
Case 20.3 Small B-cell lymphoma/follicular lymphoma
Case 20.4 Double-hit lymphoma
Case 20.5 Double-hit lymphoma with BCL6 rearrangement
Case 20.6 Plasma cell neoplasm
Case 20.7 ALK-positive large B-cell lymphoma
Case 20.8 Burkitt lymphoma (BL)
Case 20.9 High-grade B-cell lymphoma with t(8;22)(q24;q11)/IGL::MYC fusion and JAK2 rearrangement
Summary of key learning points
References
21: Mature T-cell neoplasms
Abstract
Background
Case 21.1 T-cell prolymphocytic leukemia (T-PLL)
Case 21.2 Mycosis fungoides/Sezary syndrome (MF/SS)
Case 21.3 T-cell leukemia/lymphoma with TRB rearrangement
Case 21.4 Peripheral T-cell lymphoma with TRA/TRD rearrangement
Summary of key learning points
References
Part III: Solid tumors
22: Lung cancer
Abstract
Background
Case 22.1 Pulmonary adenocarcinoma with ALK::EML4 fusion
Case 22.2 Pulmonary adenocarcinoma with EGFR p.(L858R) mutation
Case 22.3 Squamous cell carcinoma with MET exon 14 skipping mutation
Case 22.4 Pulmonary adenocarcinoma with KRAS p.(G12C) mutation
Case 22.5 Pulmonary adenocarcinoma with ERBB2 exon 20 insertion
Case 22.6 Pulmonary adenocarcinoma with TPM3::NTRK1 fusion
Summary of key learning points
References
23: Colorectal cancer
Abstract
Background
Case 23.1 Metastatic colon cancer with BRAF p.(V600E) mutation
Case 23.2 Metastatic colon cancer with KRAS p.(G12D) mutation
Summary of key learning points
References
24: Melanoma
Abstract
Background
Case 24.1 Metastatic melanoma with BRAF p.(V600K) mutation
Case 24.2 Metastatic melanoma with NRAS p.(Q61L) mutation
Summary of key learning points
References
25: Breast cancer
Abstract
Background
Case 25.1 Invasive ductal carcinoma of breast origin with HER2 amplification
Case 25.2 Adenocarcinoma of breast origin with PIK3CA p.(E545K) mutation
Case 25.3 Adenocarcinoma of breast origin with PIK3CA p.(E545K) mutation and FGFR1 amplification
Summary of key learning points
References
26: Thyroid cancer
Abstract
Background
Case 26.1 Anaplastic thyroid carcinoma with BRAF p.(V600E) mutation
Case 26.2 Malignant thyroid cancer with KRAS p.(G12V) mutation
Summary of key learning points
References
27: Pediatric solid tumors
Abstract
Background
Case 27.1 Ewing sarcoma (ES)
Case 27.2 CIC-DUX fusion-associated sarcoma
Case 27.3 Rhabdomyosarcoma
Case 27.4 NTRK1-associated sarcoma
Case 27.5 Aneurysmal bone cyst
Case 27.6 Lipoblastoma
Case 27.7 Pleuropulmonary blastoma-DICER1-associated tumors
Case 27.8 Malignant peripheral nerve sheath tumor (MPNST)-Neurofibromatosis type 1
Case 27.9 Neuroblastoma
Summary of key learning points
References
Index
Case Index

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Cases in Laboratory Genetics and Genomics (LGG) Practice

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Xia Li