How Experts Make a Call: Copy Number Variation Analysis in Unusual/Rare Case Scenarios

Background

Cytogenetic microarray (CMA) has brought a revolution in the field of cytogenetics by improving resolution by 500 times that of traditional karyotyping. Analysis and interpretation of whole genome copy number variations (CNVs) is quite a challenging task for clinicians. Some software packages and databases are available which are based on algorithm. However, there is no clear rule to decide the pathogenicity.

Objective

To formulate a step-wise approach to evaluate the interpretation of a CNV and to help the clinicians to interpret the CNV reported by a laboratory with help of four representative cases of different phenotypes.

Methods and Material

CMA was done using AffymetrixCytoscan 750K array in four cases from different families. Analysis was done based on the proposed approach.

Results

The prediction of the effect of these CNVs depends on multiple factors and can change over time as the databases are expanded. CMA in four cases from different families revealed, a rare co-occurrence of 22q13.3 duplication and 22q13.3 deletion in a proband, a deletion along with mosaicism on 10q21.2 and 10p15.3, respectively, in the second case. Third case resulted in one variant of unknown significance of 1.2 Kb deletion on 10q11.22 and the fourth case showed a benign CNV. All CNVs were analyzed based on the proposed approach and helped in subsequent management and counselling of the families. The results indicate the effectiveness of a principled, feature-based, statistical framework for uncharacterized CNV interpretation, which future studies can expand upon to construct more reliable classifiers.

Estimation of minimally important differences and responder definitions for EORTC QLQ-MY20 scores in multiple myeloma patients

Objectives

Thresholds for the minimally important difference (MID) or responder definition (RD) in health‐related quality‐of‐life (HRQoL) scores are required to interpret the impact of an intervention or change in the trajectory of the condition which is meaningful to patients. This study aimed to establish MID and RD for the European Organisation for Research and Treatment of Cancer Quality of Life Multiple Myeloma questionnaire (EORTC QLQ‐MY20).

Methods

A novel mixed‐methods approach was applied by utilizing both existing clinical trial data and prospective patient interviews. Anchor‐based, distribution‐based, and qualitative‐based estimates of meaningful change were triangulated to form recommended RDs for each scale of the EORTC QLQ‐MY20. Anchor‐based MIDs were summarized using weighted correlation.

Results

Recommended MIDs were as follows: Disease Symptoms (DS 10 points), Side Effects of Treatment (SE 10 points), Body Image (BI 13 points), and Future Perspective (FP 9 points). Recommended RDs were as follows: DS (16 improvement; 11 worsening), SE (6 improvement; 9 worsening), BI (33 improvement; 33 worsening), and FP (11 improvement; 11 worsening).

Conclusions

The study generated estimates of the MID and RD for each scale of the EORTC QLQ‐MY20. Published estimates will enable investigators and clinicians to adopt these as standard for interpretation and for hypothesis testing. Consequently, analyses from trials of different interventions can be more comparable.