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It is advocated that heterotaxy should be segregated into right or left isomerism according to atrial appendage morphology. However, atrial situs determination is often based on the pattern of associated findings rather than on atrial morphology itself, which can be difficult to define. The objective was to assess how often concordant patterns of isomerism classified by atrial appendage morphology, bronchopulmonary pattern, and splenic status are breached using cardiac magnetic resonance or computed tomography. The secondary objective was to determine the feasibility of defining atrial appendage morphology using cardiac magnetic resonance or computed tomography.Retrospective review of 114 pediatric patients (median, 2.4 years; range, 1 day–17.9 years) with heterotaxy who underwent cardiac magnetic resonance or computed tomography was performed to evaluate atrial appendage, bronchopulmonary, and visceral organ arrangements. Atrial appendage and splenic anatomy were not definable in 17 of 114 (15%) and 4 of 114 (3.5%) patients, respectively. In the remaining 93 patients, 39% had classic right isomerism (bilateral right atrial appendages, right bronchopulmonary pattern, and asplenia) and 40% had classic left isomerism (bilateral left atrial appendages, left bronchopulmonary pattern, and polysplenia). Classic pattern of isomerism was breached in 20 of 93 (21.5%) patients: 13 (65%) displayed incongruent abdominal situs, 5 (25%) incongruent bronchial situs, 1 (5%) had discrepant appendage morphology, and 1 (5%) incongruent situs at all levels.Atrial appendage morphology is difficult to assess and not always indicative of bronchopulmonary or abdominal situs. Discordance between bronchopulmonary branching, atrial appendage arrangement, and splenic status was identified in >20% patients with heterotaxy. Independent description of each organ system is required when arrangements are disharmonious among different organ systems.