Germline-focussed analysis of tumour-only sequencing: recommendations from the ESMO Precision Medicine Working Group

It is increasingly common in oncology practice to perform tumour sequencing using large cancer panels. For pathogenic sequence variants in cancer susceptibility genes identified on tumour-only sequencing, it is often unclear whether they are of somatic or constitutional (germline) origin. There is wide-spread disparity regarding both the extent to which systematic 'germline-focussed analysis' is carried out upon tumour sequencing data and for which variants follow-up analysis of a germline sample is carried out. Here we present analyses of paired sequencing data from 17 152 cancer samples, in which 1494 pathogenic sequence variants were identified across 65 cancer susceptibility genes. From these analyses, the European Society of Medical Oncology Precision Medicine Working Group Germline Subgroup has generated (i) recommendations regarding germline-focussed analyses of tumour-only sequencing data, (ii) indications for germline follow-up testing and (iii) guidance on patient information-giving and consent.

On the changed composition of an anorthoclase-bearing rock-glass

The present investigation began with an attempt to isolate and analyse the small sparse anorthoclase insets (t)henocrysts) of the chilled glassy selvage of a felsite dike. On comparison of the compositions of the insets and the host rock it was found that the relationship was abnormal and that the insets could not have grown in a magma represented by the glass. The composition of the felsite interior of the dike, however, represents a magma which could have yielded the anorthoclase, and full consideration leads to the conclusion that the glass, though absolutely fresh and unaltered in appearance, has suffered marked changes in composition.

Time-allocation, matching, and contrast

A variable-interval schedule arranged food reinforcement for key pecking by pigeons on a single operandum at two rates, corresponding to two classes of reinforced interresponse times ranging from 1.5 to 2.5 sec and from 3.5 to 4.5 sec. The scheduled reinforcement rate for the higher component response rate was constant and equivalent to that of a variable-interval 4-min schedule. The scheduled reinforcement rate for the lower component response rate varied from zero to over 100 per hour. The number of occurrences of the constant component response rate varied inversely with the reinforcement rate for the variable component. This result, by definition a concurrent reinforcement interaction, or contrast, was the combined effect of two time-allocation functions, which together determine mean response rate: the time allocated to both component rates as a function of the total reinforcement rate, and the time allocated to a particular component rate as a function of the percentage of reinforcements for that component. The present experiment reveals a further parallel between the controlling relations for free responding on a single operandum and those for choice between two operanda; in each case, a concurrent reinforcement interaction can be found that corresponds to matching.

Choice between response rates

Three pigeons were required to peck a single key at a higher and a lower rate, corresponding to two classes of shorter and longer concurrently reinforced interresponse times. Food reinforcers arranged by a single variable-interval schedule were randomly allocated to the two reinforced interresponse times. The absolute durations of reinforced interresponse times were varied while the total reinforcements per hour was held constant and the relative duration, i.e., the relative reciprocal, of the shorter reinforcer class was held constant at 0.70. Preference for the higher rate of responding, as measured by the relative frequency of responses terminating interresponse times in the shorter reinforced class, depended on the absolute reinforced response rates. Preference for the higher reinforced rate increased from a level of near-indifference (0.50) at high reinforced response rates, through the matching level (0.70) at intermediate reinforced response rates, to a virtually exclusive preference (>0.90) at low reinforced response rates. These results resemble corresponding preference functions obtained with two-key concurrent-chains schedules and thereby provide another sense in which it may be said that interresponse-time distributions from interval schedules estimate preference functions for the component response rates corresponding to different classes of reinforced interresponse times.

Reinforcement of behavioral patterns: shaping a scallop

Temporal patterns of key pecking by pigeons were shaped by a schedule in which the delivery of food was contingent upon a measure of the overall extent to which the temporal pattern of behavior within a 5-sec trial conformed to a required pattern. This pattern approximated a constant rate of change in the rate of key pecking throughout the 5-sec trial. In comparison with behavior maintained by a classical fixed-interval 5-sec schedule, the new schedule controlled a better approximation to a "scallop" within individual trials and greatly reduced intersubject variability. These results are consistent with the view that the delivery of a reinforcer after a behavioral pattern a few seconds in duration may strengthen the entire pattern as a unit, or operant. The response topography contiguous with reinforcement may be a negligible fraction of the strengthened operant. One implication of this view is that mean response rate for such brief responses as key pecks and lever presses is a byproduct of whatever patterns are strengthened, and generally will not reveal fundamental controlling relationships, whenever a reinforcer is not contiguous with all the behavior on which it is contingent.

A simplified method for fabrication of a die holder

A technique is described for fabricating a simple and inexpensive holder for dies to be used during the process of die spacer application.