Chromosome Genomic Array Testing Research Articles

Mutational profiling in acute lymphoblastic leukemia by RNA sequencing and chromosomal genomic array testing.

BackgroundComprehensive molecular and cytogenetic profiling of acute lymphoblastic leukemia (ALL) is important and critical to the current standard of care for patients with B‐acute lymphoblastic leukemia (B‐ALL). Here we propose a rapid process for detecting gene fusions whereby FusionPlex RNA next‐generation sequencing (NGS) and DNA chromosome genomic array testing (CGAT) are combined for a more efficient approach in the management of patients with B‐ALL.MethodsWe performed RNA NGS and CGAT on 28 B‐ALL samples and, in four patients, compared fixed cell pellets to paired cryo‐preserved samples as a starting material to further assess the utility of cytogenetic fixed pellets for gene expression analysis.ResultsAmong the fixed specimens, when using alternative techniques as references, including karyotype, fluorescence in situ hybridization, CGAT, and RT‐qPCR, fusions were detected by RNA NGS with 100% sensitivity and specificity. In the four paired fixed versus fresh cryopreserved samples, fusions were also 100% concordant. Four of the 28 patients showed mutations that were detected by RNA sequencing and three of four of these mutations had well‐known drug resistance implications.ConclusionsWe conclude that FusionPlex is a robust and reliable anchored multiplex RNA sequencing platform for use in the detection of fusions in both fresh cryopreserved and cytogenetic fixed pellets. Gene expression data could only be obtained from fresh samples and although limited variant data are available, critical hotspot variants can be determined in conjunction with the fusions.

Genomic Alterations Important for the Prognosis in Patients with Follicular Lymphoma Treated on SWOG Study S0016

Background: Follicular lymphoma (FL) is a common, indolent, yet typically incurable disease characterized by clinical and genetic heterogeneity. Recent studies suggested that TNFRSF14 mutation and 1p36 deletion were associated with worse outcome in FL and that TNFAIP3 mutation on 6q occurred at FL transformation. However, no genomic biomarkers are currently in clinical use for prognostic and therapeutic decisions. We aimed to identify novel genomic aberrations associated with prognosis of patients with FL in the context of a randomized cooperative group trial (Press 2013 JCO).Patients and Methods: We employed a comprehensive genomic array testing strategy to assess the common genomic abnormalities, including copy number aberrations (CNAs), copy-neutral loss-of-heterozygosity (cnLOH), and common cancer gene mutations. Our study set includes all patients enrolled in the SWOG FL study S0016 with available pre-treatment tissue specimens. Chromosome genomic array testing (CGAT) has been performed on 255 archived formalin-fixed, paraffin embedded (FFPE) lymphoma tissue specimens. A SWOG pathologist reviewed all tissues prior to CGAT to ensure that each sample met the diagnostic criteria for FL and had at least 30% tumor content. The OncoScan platform was used for CGAT with data analysis performed by Nexus Express. Statistical analysis was performed using the Cox-proportional hazard regression model. Hazard ratio (HR) and 95% confidence interval (CI) were estimated from the multivariate model. Statistical significance was determined at an alpha-level of 0.05 after Bonferroni adjustment for multiple comparisons.Results: CGAT was successful on 247 samples (97%), and 245 entered into final data analysis. Most samples (>90%) showed multiple chromosome abnormalities (median 8, range 1-64). The most frequently affected chromosome arms were: 1p (54%), 6p (39%), 6q (38%), 18q (36%), 12q or 16p (33%), and 1q (32%). Specific common CNAs were deletions of 1p, 6q, 10q, and 17p, gains of X, 1q, 2, 7, 8q, 12, 17q, and 18, and cnLOH of 1p, 6p, and 16p. Univariate analysis for progression free survival (PFS) identified several aberrations significantly associated with prognosis at unadjusted .05 level. Multivariate analysis adjusting for FLIPI risk, bulky disease, and combined serum b2M and LDH levels demonstrated that three markers, 9p deletion or cnLOH, 12p gain, and 17q gain, remained significant for PFS (HR 2.0, 1.7, and 1.7 for 9p, 12p, and 17q, respectively). Comparing treatment arms, the hazard of progression or death is 0.6 times less comparing CHOP+I-131 vs. CHOP+R if a patient has no abnormality in Xp (P=0.02). When we further analyzed specific segmental aberrations, eight regions were independent prognostic markers for overall survival (OS) in multivariate analysis and seven regions for PFS (see Figure 1 for representative markers). Specifically, patients with abnormal CDKN2A/B (p16) were 3.2 times more likely to progress early (P<.0001) while those with abnormal TP53 (17p) and TNFRSF12A/CREBBP (16p) loci were 3.9 and 6.7 times, respectively, more likely to die early (P=0.0001). For treatment effect on OS, six patients with abnormal TNFRSF12A/CREBBP (16p) showed an HR 0.06 when receiving CHOP+I-131 compared to CHOP+R (P=0.02). In particular, comparing patients who progressed vs. not at two years, Fisher's exact test identified seven differential genomic regions. Among these, FANCL region on 2p and USP3 region on 15q were also significant (P<.005) in Cox regression analysis limiting 2-year follow-up with the goal to focus on early events.Conclusion: We confirmed the frequent 1p (TNFRSF14) and 6q (TNFAIP3) deletions in FL reported in literature. More importantly, we identified several genomic aberrations that showed independent prognostic value for FL patients. Among these, deletions and cnLOH of CDKN2A (9p), CREBBP (16p) and TP53 (17p) are of significant interest. These genomic aberrations may add to currently utilized clinical risk stratification as a means to identify high risk patients at diagnosis of FL. Certain markers that showed treatment arm effect may serve as predictive markers.Support: This work was supported by Affymetrix Inc., NIH/NCI National Clinical Trials Network (NCTN) grants CA180888 and CA180819, and in part by GlaxoSmithKline. [Display omitted] DisclosuresPress:Roche: Honoraria, Research Funding; BMS: Honoraria; Bayer: Consultancy. Hsi:Seattle Genetics: Consultancy, Honoraria, Speakers Bureau; Cellerant Therapeutics: Research Funding; Abbvie: Research Funding; Eli Lilly and Co.: Research Funding. Leonard:Celgene: Consultancy, Research Funding; Roche: Consultancy. Friedberg:Bayer HealthCare Pharmaceuticals.: Other: Data and Safety Monitoring Board: Bayer HealthCare Pharmaceuticals.

Pembrolizumab with R-CHOP in Previously Untreated Diffuse Large B-Cell Lymphoma: Long Term Follow up and Analysis of the Mechanism of Pdl-1 Tumor Expression

Pembrolizumab with R-CHOP in Previously Untreated Diffuse Large B-Cell Lymphoma: Long Term Follow up and Analysis of the Mechanism of Pdl-1 Tumor Expression

Genomic alterations important for the prognosis in patients with follicular lymphoma treated in SWOG study S0016

AbstractAlthough recent advances in molecular genetics have enabled improved risk classification of follicular lymphoma (FL) using, for example, the m7-FLIPI score, the impact on treatment has been limited. We aimed to assess the prognostic significance of copy-number aberrations (CNAs) and copy-neutral loss of heterozygosity (cnLOH) identified by chromosome genomic-array testing (CGAT) at FL diagnosis using prospectively collected clinical trial specimens from 255 patients enrolled in the SWOG study S0016. The impact of genomic aberrations was assessed for early progression (progressed or died within 2 years after registration), progression-free survival (PFS), and overall survival (OS). We showed that increased genomic complexity (ie, the total number of aberration calls) was associated with poor outcome in FL. Certain chromosome arms were critical for clinical outcome. Prognostic CNAs/cnLOH were identified: whereas early progression was correlated with 2p gain (P = .007; odds ratio [OR] = 2.55 [1.29, 5.03]) and 2p cnLOH (P = .005; OR = 10.9 [2.08, 57.2]), 2p gain specifically encompassing VRK2 and FANCL predicted PFS (P = .01; hazard ratio = 1.80 [1.14, 2.68]) as well as OS (P = .005; 2.40 [1.30, 4.40]); CDKN2A/B (9p) deletion correlated with worse PFS (P = .004, 3.50 [1.51, 8.28]); whereas CREBBP (16p) (P < .001; 6.70 [2.52, 17.58]) and TP53 (17p) (P < .001; 3.90 [1.85, 8.31]) deletion predicted worse OS. An independent cohort from the m7-FLIPI study was explored, and the prognostic significance of aberration count, and TP53 and CDKN2A/B deletion were further validated. In conclusion, assessing genomic aberrations at FL diagnosis with CGAT improves risk stratification independent of known clinical parameters, and provides a framework for development of future rational targeted therapies.

Clinical Utility of Chromosome Genomic Array Testing for Unclassified and Advanced-Stage Renal Cell Carcinomas.

Cytogenomic analysis provides a useful adjunct to traditional pathology in the categorization of renal cell carcinomas (RCCs), particularly in morphologically ambiguous cases, but it has disadvantages, including cost. To define the clinical scenarios in which this technology has direct clinical applications. DNA was isolated from paraffin-embedded tissue from 40 selected cases of RCC. Chromosome genomic array testing was performed using the OncoScan. Of 23 cases of unclassified renal tumors, 19 (83%) were reclassified with incorporation of cytogenetic and histologic features, including 10 as clear cell RCC, 2 as collecting duct carcinoma, 2 as papillary RCC, and 1 as novel TFEB-amplified tumor lacking TFEB translocation. Of 5 tumors with "hybrid" oncocytic features, 3 were reclassified as an eosinophilic variant of chromophobe RCC and 1 as oncocytoma. Appropriate staging in 2 patients was determined by identifying distinct, nonshared cytogenetic profiles. Of 11 cases of metastatic clear cell RCC, 7 (63%) had cytogenetic features associated with a poor prognosis. We identified 5 scenarios in which chromosome genomic array testing has direct clinical utility: (1) to investigate unclassified RCCs, (2) to understand tumors with "hybrid" features and "collision" tumors, (3) to determine appropriate staging in questions of bilateral tumors and/or metastases, (4) to identify chromosomal aberrations in metastatic clear cell RCCs associated with a worse prognosis, and (5) to identify new entities. This has practical value in our institution, where a molecular profile diagnostically separating morphologically difficult to classify clear cell, papillary, chromophobe, and unclassified RCC influences treatment recommendations and clinical trial eligibility.

36 - CD138 Enrichment Strategy and Results of Chromosome Genomic Array Testing (CGAT) for Multiple Myelomas

36 - CD138 Enrichment Strategy and Results of Chromosome Genomic Array Testing (CGAT) for Multiple Myelomas

Jumping translocations in myelodysplastic syndromes

Jumping translocations (JT) have been identified in numerous malignancies, including leukemia, but infrequently in patients with myelodysplastic syndromes (MDS). The responsible genetic region has been mapped to the JTB gene at 1q21, but breakpoints involving other chromosomal loci, such as 3q and 11q, have been described as well. We have characterized the pathological and mutational landscape, and the clinical course of 6 new MDS patients with jumping mutations using chromosome genomic array testing (CGAT) and target gene panel next generation sequencing. In addition, we have performed a literature review for other MDS cases with JTs as defined by ISCN 2013. Results support the concept that MDS in patients with jumping translocations has a poor prognosis with a high risk of progression to leukemia, and suggest that these patients warrant aggressive therapy, including HCT, early in the disease course.

Association of treatment for late-onset tMDS with glioblastoma recurrence in a patient displaying long-term disease response and survival.

e13506Background: Gene therapy with autologous, mutant methylguanine methyltransferase (MGMT) modified blood cells prevents myelosuppression from O6-benzylguanine and temozolomide (O6BG/TMZ) chemot...

Jumping Translocations in Myelodysplastic Syndromes

Jumping translocations (JT) have been identified in numerous malignancies, including leukemia, but infrequently in patients with myelodysplastic syndromes (MDS). The responsible genetic region has been mapped to the JTB gene at 1q21, but breakpoints involving other chromosomal loci, such as 3q and 11q, have been described as well. We have characterized the pathological and mutational landscape, and the clinical course of 6 new MDS patients with jumping mutations using chromosome genomic array testing (CGAT) and target gene panel next generation sequencing. In addition, we have performed a literature review for other MDS cases with JTs as defined by ISCN 2013. Results support the concept that MDS in patients with jumping translocations has a poor prognosis with a high risk of progression to leukemia, and suggest that these patients warrant aggressive therapy, including HCT, early in the disease course.

Genomic Alterations Important for the Prognosis in Patients with Follicular Lymphoma Treated on SWOG Study S0016

Background: FL is a common, indolent, yet typically incurable disease characterized by clinical and genetic heterogeneity. Recent studies suggested that TNFRSF14 mutation and 1p36 deletion were associated with worse outcome in FL and that TNFAIP3 mutation on 6q occurred at FL transformation. However, no genomic biomarkers are currently in clinical use for prognostic and therapeutic decisions. We aimed to identify novel genomic aberrations associated with prognosis of patients with FL in the context of a randomized cooperative group trial (Press 2013 JCO).Patients and Methods: We employed a comprehensive genomic array testing strategy to assess the common genomic abnormalities, including copy number aberrations (CNAs), copy-neutral loss-of-heterozygosity (cnLOH), and common cancer gene mutations. Our study set includes all patients enrolled in the SWOG FL study S0016 with available pre-treatment tissue specimens (n=250). To date, chromosome genomic array testing (CGAT) has been performed on archived formalin-fixed, paraffin embedded (FFPE) lymphoma tissue specimens from 158 patients. A SWOG pathologist reviewed all tissues prior to CGAT to ensure that each sample met the diagnostic criteria for FL and had at least 30% tumor content. The OncoScan platform was used for CGAT with data analysis performed by Nexus Express. Statistical analysis was performed using the Cox-proportional hazard regression model. Hazard ratio (HR) and 95% confidence interval (CI) were estimated from the multivariate model. For this exploratory analysis, statistical significance was determined at an alpha-level of 0.05 without adjustment for multiple comparisons.Results: Most samples (>90%) showed multiple chromosome abnormalities (median 10, range 1-65). The most frequently affected chromosome arms were: 1p (49.3%), 6q (41.7%), 6p (40.5%), 1q (38.6%), 16p or 22q (36%), and 18q (35.4%). Specific common CNAs were deletions of 1p, 6q, and 10q, gains of X, 1q, 2p, 7, 8q, 12q, 17q, and 18, and cnLOH of 1p, 6p, and 16p. Point mutations were not identified. Univariate analysis for progression free survival (PFS) identified several aberrations (of the 94 aberrations assessed) significantly associated with prognosis at unadjusted .05 level; these include gain of 12p, 17q, 18q, and Yp, deletions of 2q, 6q, 8q, 9p, and Yq, and deletion or cnLOH of 9p and 10q. Multivariate analysis adjusting for FLIPI risk, bulky disease, and combined serum β2M and LDH levels demonstrated that selected markers, including deletion or cnLOH of 9p and 10q and gain of 12p and 17q, remained significant for PFS (HR 2.0 for 9p, 0.5 for 10q, 2.8 for 12p, and 2.0 for 17q), while FLIPI risk and serum β2M/LDH levels were no longer significant. In particular, estimated two-year PFS was lower in patients with 9p deletion or cnLOH (60% vs 77%), gain of 12p (62% vs 78%), and gain of 17q (59% vs 80%) compared with those without.Conclusion: We confirmed the frequent 1p and 6q deletions in FL reported in literature. In addition, we identified several genomic aberrations that may be prognostic of FL patients. Among these, deletions and cnLOH of CDKN2A (9p), PTEN (10q) and CREBBP (16p) are of significant interest for their known tumor suppressor functions. Gain of 12p, 17q, and 18q may also help identify oncogenes and other activating tumorigenic processes relevant to disease progression and survival. Multivariate analysis suggested that the genomic aberrations might add to currently utilized clinical risk stratification as a means to identify high risk patients at diagnosis of follicular lymphoma.Support: This work was supported by Affymetrix Inc., NIH/NCI National Clinical Trials Network (NCTN) grants CA180888 and CA180819, and in part by GlaxoSmithKline. DisclosuresHsi:Abbvie: Research Funding; Cellerent Therapeutics: Research Funding; Eli Lilly: Research Funding; Onyx: Honoraria; Seattle Genetics: Honoraria. Smith:Pharmacyclics: Consultancy; Celgene: Consultancy. Fang:Affymetrix: Research Funding.

Prognostic significance of acquired copy-neutral loss of heterozygosity in acute myeloid leukemia.

Chromosomal abnormalities are important in the diagnosis and prognosis of patients with acute myeloid leukemia (AML). Genomic microarray techniques detect recurrent copy-neutral loss of heterozygosity (cnLOH) in addition to copy number aberrations. However, the clinical utility has not been fully established. Therefore, in the current study, the authors examined the prognostic impact of acquired cnLOH in patients with AML, including complete remission (CR) rate, duration of CR, and overall survival (OS). A total of 112 consecutive patients with AML who were undergoing chromosome genomic array testing (CGAT) at the Seattle Cancer Care Alliance were included in the current study. DNA from the bone marrow or blood was analyzed with a microarray platform with both single-nucleotide polymorphism (SNP) probes and non-SNP probes to identify acquired cnLOH. Results were correlated with cytogenetic, molecular, immunophenotypic, and other clinicopathological findings. Patients with cnLOH demonstrated a shorter duration of CR (hazard ratio, 1.87; P =.04) and worse OS (HR, 1.82; P = .03). Multivariate analyses confirmed the independent predictive value of cnLOH for early disease recurrence (P =.02). These results largely reflected those in patients with intermediate and unfavorable cytogenetics. Most strikingly, 13q cnLOH was found to demonstrate a 6.64-fold higher rate of disease recurrence (P =.006) and 3.45-fold worse OS (P = .02) and was enriched with the FLT3-ITD (Fms-related tyrosine kinase 3-internal tandem duplication) mutation. CnLOH has important prognostic significance in patients with AML. CGAT can replace imbalance fluorescence in situ hybridization and the authors recommend the routine use of CGAT to detect cnLOH, particularly among patients with intermediate-risk cytogenetics.

Proof-Of-Concept Study For Precision Medicine With Chromosome Genomic Array Testing (CGAT) For Drug Sensitivity Screening In Acute Myeloid Leukemia

Tremendous heterogeneity in acute myeloid leukemia (AML) poses a significant challenge to clinical management and effective therapy. Cytogenetics is one of the key prognostic factors for AML. New technologies, such as chromosome genomic array testing (CGAT) combining both SNP-based and non-SNP based array CGH, have allowed informative genomic profiling of chromosome abnormalities with very high resolution. Yet it remains unclear how these unique CGAT-identified clonal aberrations impact the outcome of AML patients and how they predict a patient's response to a specific medication. In this proof-of-concept study, we aim to explore the correlation of genomic abnormalities identified by CGAT with in vitrodrug sensitivity data from 30 AML patients and their clinical responses.We performed CGAT on the pre-treatment bone marrow of these AML patients using CytoScanHD, which includes 2.5 million markers, 750K of which are SNP markers. Copy number aberrations (CNA) and copy-neutral loss of heterozygosity (cnLOH) were analyzed by ChAS and Nexus software. CGAT abnormalities were enumerated based on chromosome arms affected; i.e., multiple segmental CNAs and cnLOH on the same chromosome arm were counted as one aberration. Patients' response to chemotherapy and clinical relapse were tracked. Drug sensitivity for individual patient leukemia blast samples was measured by a high-throughput in vitroassay consisting of a panel of 160 drugs, of which 45 are FDA approved and 115 investigational. Cell survival was measured by Cell Titer Glo, and data curves for 8 concentrations of each drug were generated to derive EC50 and IC50 values. Statistical correlation was analyzed by Fisher's exact test, Cox regression, and regression analysis.CGAT detected all the chromosome abnormalities identified by cytogenetics except truly balanced translocations. CGAT also identified clonal aberrations in 7 of the 13 patients with normal cytogenetics. Of the 6 uniquely CGAT abnormal patients, 3 demonstrated cnLOH only and 2 CNA only. Overall, CGAT showed 11 complex karyotypes (CK, defined as >=3 aberrations; high-risk) and 19 normal or simple abnormal cases (low/intermediate-risk), as compared to the cytogenetics classification of 9 poor-risk, 15 intermediate-risk, and 6 low-risk karyotypes. cnLOH was detected in 9 patients (30%). Complete remission (CR) rate after the first induction course in the CGAT CK group was 18% versus 68% in the non-CK group (P=0.02). There was a very high concordance (90%) between CGAT risk based on CK and conventional cytogenetics. And when cytogenetics and CGAT disagree, as for the 2 patients who had normal cytogenetics but CGAT CK, CGAT risk stratification appeared better as neither patient achieved CR. CR duration longer than 1 year occurred more (P=0.04) in the CGAT normal patients (50%) than in the CGAT abnormal patients (8.3%). Among those who achieved CR, the hazard of relapse (HR) for CGAT CK patients was 9.9 (CI: 1.6-61; P=0.02); HR for cnLOH patients was 7.1 (CI: 1.2-43; P=0.03). Considering the total aberrations (median 1.5, range 0-16), the HR for relapse among CR patients was 1.3 (CI: 1.1-1.5; P=0.01) per aberration. Six of the 48 drugs that exhibited cytotoxicity in the in vitro assay, including clofarabine (r=0.45, P=0.01) and PKI-587 (dual PI3K/mTOR inhibitor) (r=0.48, P=0.008), showed significant correlation between CGAT aberrations and EC50; i.e, the more CGAT aberrations, the higher concentration is required for a given drug to kill these CGAT-abnormal leukemic cells in vitro.In conclusion, CGAT increased the diagnostic yield by 54% among AML patients with normal cytogenetics and altered the overall risk classification by 6.7%. Complex karyotype identified by CGAT carried the same poor prognostic effect as CK by cytogenetics. Although abnormal CGAT results did not appear to predict response, increasing CGAT abnormalities are associated with early relapse, as is the presence of cnLOH. Genomic complexity detected by CGAT appeared to associate with dosage-dependent resistance to selected drugs by in vitro drug sensitivity analyses. Characterization of prognostic effect and drug response associated with each type of CGAT abnormalities will require a larger data set. Nevertheless, this study demonstrated the clinical utility of CGAT for precision medicine in AML. Disclosures:Becker:Affymetrix: Research Funding.

6-OR

A 25 year old male AML patient in relapse was refered to our transplant center, having undergone a haploidentical transplant from a sib at another center. Bone marrow was collected, DNA from the sorted blast fraction isolated and HLA typed using rSSO (Luminex). Only the paternal haplotype shared with the sibling donor was detected in the blast cells, suggesting loss of heterozygosity (LOH), since both the patient’s original maternal haplotype and the donor’s unshared haplotype were absent. Chimerism testing confirmed that the blast cells were entirely of patient origin. Buccal sample DNA was HLA typed and the patient’s original germline type was confirmed. We decided to run both marrow and buccal samples by chromosome genomic array testing (CGAT) to confirm our HLA results. DNA from the blast fraction was isolated using QIAamp DNA Blood MiniKit; DNA from the buccal sample was isolated using QIAamp DNA MicroKit. Both samples were run in Luminex rSSO assays. CytoScanHD (Affymetrix) was run using DNA from unsorted bone marrow (Qiagen Gentra Puregene kit) and the results compared with the genomic profile obtained using the buccal sample DNA. Only the paternal haplotype was detected by Luminex rSSO in the DNA from the blast fraction (A*33:03g, C*16:02g, B*51:08g, DRB1*12, DQB1*03:01g), while both paternal and maternal haplotypes were present in buccal DNA. For whole bone marrow cells, the CGAT array plot clearly showed copy neutral LOH on the short arm of chromosome 6 from 6p21.2 to the telemere. For the buccal cells, the CGAT profile showed no LOH for the “virtual karyotype” of chromosome 6. Both HLA and CGAT assays confirmed LOH for the entire HLA region on the short arm of chromosome 6 in this patient’s blast cells, an example of copy number neutral acquired uniparental disomy. The graphic output of the CGAT dramatically illustrates this acquired somatic mutation.

4-OR

Saliva is fast becoming an alternative to buccal cells as a source of DNA for HLA typing prior to hematopoietic cell transplant (HCT), either when a peripheral blood sample is not an option or as a source of germline DNA. We describe the case of a 47 year old male aplastic anemia patient, previously typed at another center and subsequently referred to our center for HLA typing. Initial SBT on saliva and peripheral blood lymphocytes showed dropout of the expected maternal haplotype. A buccal swab sample was obtained for further typing. Saliva was collected using an Oragene kit and DNA extracted with the QIAgen EZ1 DNA Tissue kit. Buccal cells were collected using sterile swabs (Cap-Shure) and DNA extracted using QIAamp DNA microkit. HLA typing was performed by SBT with Atria reagents on an ABI 3130xl and analyzed with Conexio Assign software. Both samples were also tested with rSSO and by Chromosome Genomic Array Testing (CGAT). Initial typing of the patient’s saliva sample by SBT generated the type A*03:01, C*04:JERF, B*XX, DRB1*01:01 (with possible 2nd alleles at A, C, and DRB1). Based on external typing, it appeared that the patient had lost the maternal haplotype, suggesting loss of heterozygosity (LOH), confirmed by CGAT “virtual keryotyping” of chromosome 6, which also revealed copy neutral uniparental disomy. The array plot clearly showed ∼40Mb LOH from 6p21.1 to the telemere, which included the entire HLA region. Typing of buccal sample revealed a heterozygous A*03:01, 02:01, C*04:JERF, 02:02, B*35:BJTR, B*27:EKN, DRB1*01:01, 09:01 type. Since this aplastic anemia patient had never been transplanted, the LOH must have occurred at some time between the initial external typing and our more recent typing. This case indicates that caution must be used even when testing patients who do not suffer from hematological malignancies, especially when relying on saliva samples as a DNA source for either germline sample or for confirmatory HLA typing.

Unique Challenges and Discoveries From Chromosome Genomic Array Testing (CGAT) in the Setting of Hematopoietic Cell Transplantation

The clinical utility of chromosome genomic array testing (CGAT) is increasingly appreciated for cancer diagnosis. The detection of copy number aberrations (CNAs) and copy-neutral LOH (cnLOH) significantly enhance diagnostic yield and provide for additional prognostic information. In the setting of hematopoietic cell transplantation (HCT), unique challenges of detecting pre- or post-transplant minimal residual disease (MRD) and post-transplant mixed chimerism provide opportunities for innovative methodologies, appropriate interpretation of results, and novel discoveries.